4NPC | pdb_00004npc

Crystal Structure of an Oxidoreductase, Short-Chain Dehydrogenase/Reductase Family Protein from Brucella suis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EGF	PDB entry 4EGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	MCSG1(f5): 0.2M Sodium Acetate, 20% PEG-3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.74	α = 90
b = 87.74	β = 90
c = 117	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2013-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	70.19	99.6	0.042	29.71	7	46707	46513		-3	29.873

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	99.9		0.493	4.06

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4EGF	1.75	50	48865	46512	2353	99.58	0.1506	0.1487	0.16	0.1871	0.2	RANDOM	26.4

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]
-0.41			-0.41		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.712
r_dihedral_angle_4_deg	15.373
r_dihedral_angle_3_deg	12.819
r_dihedral_angle_1_deg	6.092
r_angle_refined_deg	1.497
r_mcangle_it	1.391
r_mcbond_it	0.931
r_mcbond_other	0.928
r_angle_other_deg	0.809
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.712
r_dihedral_angle_4_deg	15.373
r_dihedral_angle_3_deg	12.819
r_dihedral_angle_1_deg	6.092
r_angle_refined_deg	1.497
r_mcangle_it	1.391
r_mcbond_it	0.931
r_mcbond_other	0.928
r_angle_other_deg	0.809
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3614
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.