8rxn: Difference between revisions

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[[Image:8rxn.jpg|left|200px]]<br /><applet load="8rxn" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:8rxn.jpg|left|200px]]<br /><applet load="8rxn" size="350" color="white" frame="true" align="right" spinBox="true"

caption="8rxn, resolution 1.0Å" />

'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''<br />

==Overview==

X-ray data have been recorded from crystals of rubredoxin derived from the, bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part, synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha, source. In both cases an imaging-plate scanner was used as detector. The, space group of the crystals is P2(1) with cell dimensions a = 19.97, b =, 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I), factor between symmetry-related reflections was 5.8%. The model was, refined by least-squares minimization initially with stereochemical, restraints to an R factor of 16.4%. Only atomic positional parameters and, isotropic temperature factors for non-H atoms were used in the refinement., There were 18,532 independent X-ray observations for a total of 1916, atomic parameters. A round of unrestrained refinement gave an R factor of, 16.0%, acceptable geometry for more than 90% of the protein atoms, but, emphasized the disorder inherent in eight of the residues. A final round, of restrained refinement gave an R factor of 14.7%. Three of the 389, protein atoms in the molecule, in the side chain of Lys2, have been, assigned zero occupancy in the model. A total of eight atoms in three side, chains have been assigned two conformations, giving 393 protein atomic, sites in the model. In addition there is one Fe atom, a sulfate ion and, 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal, motion. This has not been incorporated in the present model.

X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.

==About this Structure==

8RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].

8RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].

==Reference==

Line 20:

[[Category: electron transport(iron)]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Tue Nov 20 13~~:01:~~08 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:18:18 2008''

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@@ Line 1: / Line 1: @@
-[[Image:8rxn.jpg|left|200px]]<br /><applet load="8rxn" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:8rxn.jpg|left|200px]]<br /><applet load="8rxn" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="8rxn, resolution 1.0&Aring;" />
 '''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''<br />
 ==Overview==
-X-ray data have been recorded from crystals of rubredoxin derived from the, bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part, synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha, source. In both cases an imaging-plate scanner was used as detector. The, space group of the crystals is P2(1) with cell dimensions a = 19.97, b =, 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I), factor between symmetry-related reflections was 5.8%. The model was, refined by least-squares minimization initially with stereochemical, restraints to an R factor of 16.4%. Only atomic positional parameters and, isotropic temperature factors for non-H atoms were used in the refinement., There were 18,532 independent X-ray observations for a total of 1916, atomic parameters. A round of unrestrained refinement gave an R factor of, 16.0%, acceptable geometry for more than 90% of the protein atoms, but, emphasized the disorder inherent in eight of the residues. A final round, of restrained refinement gave an R factor of 14.7%. Three of the 389, protein atoms in the molecule, in the side chain of Lys2, have been, assigned zero occupancy in the model. A total of eight atoms in three side, chains have been assigned two conformations, giving 393 protein atomic, sites in the model. In addition there is one Fe atom, a sulfate ion and, 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal, motion. This has not been incorporated in the present model.
+X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.
 ==About this Structure==
-RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].
+RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].
 ==Reference==
@@ Line 20: / Line 20: @@
 [[Category: electron transport(iron)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:01:08 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:18:18 2008''