7KOM | pdb_00007kom

High Resolution Crystal Structure of Putative Pterin Binding Protein PruR (VV2_1280) from Vibrio vulnificus CMCP6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	292	Protein: 7.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (A7), 0.1M Citric acid (pH 3.5), 3.0M Sodium chloride. Cryo: 4.0M Formate

Crystal Properties
Matthews coefficient	Solvent content
2	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.046	α = 90
b = 71.087	β = 90
c = 106.359	γ = 90

Symmetry
Space Group	I 2 2 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	Be	2018-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	0.99	30	93.4	0.075	0.075	0.081	0.03	45.1	7.3		65367		-3	6.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.99	1.01	82.2		0.679	0.679	0.74	0.288	0.821	3.2	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	0.99	26.6	62187	3176	93.21	0.1205	0.1195	0.12	0.141	0.14	RANDOM	9.117

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]
-1.07			0.61		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.417
r_dihedral_angle_4_deg	13.304
r_dihedral_angle_3_deg	9.826
r_rigid_bond_restr	9.196
r_dihedral_angle_1_deg	4.926
r_angle_refined_deg	1.53
r_angle_other_deg	1.389
r_chiral_restr	0.084
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.417
r_dihedral_angle_4_deg	13.304
r_dihedral_angle_3_deg	9.826
r_rigid_bond_restr	9.196
r_dihedral_angle_1_deg	4.926
r_angle_refined_deg	1.53
r_angle_other_deg	1.389
r_chiral_restr	0.084
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1098
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.