1RB9 | pdb_00001rb9

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS REFINED ANISOTROPICALLY AT 0.92 ANGSTROMS RESOLUTION

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8RXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
1.64	25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 19.97	α = 90
b = 41.45	β = 108.3
c = 24.41	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH	MIRRORS	1988-08-05	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		EMBL/DESY, HAMBURG	X31

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	0.92	20	98.5	0.031	0.031	10	3.7		26124		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	0.92	0.94	98		0.148	0.148	3.1	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MODEL KNOWN (8RXN)	8RXN	0.92	20	48061		98.5	0.0731		0.08

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
12	524	1426.6

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.24
s_zero_chiral_vol	0.153
s_approx_iso_adps	0.102
s_similar_adp_cmpnt	0.04
s_angle_d	0.038
s_similar_dist	0.031
s_bond_d	0.021
s_rigid_bond_adp_cmpnt	0.007
s_from_restr_planes
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	716
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SHELXL-97	model building
SHELXL-97	refinement
MOSFLM	data reduction
Agrovata	data scaling
SHELXL-97	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.