7KOU

1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KOM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: JCSG+ (F8), 2.1M DL-Malic acid pH 7.0; Cryo: 25% PEG 400, 1.5M DL-Malic acid pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.928	α = 90
b = 62.022	β = 90
c = 101.916	γ = 90

Symmetry
Space Group	P 21 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	Be	2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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)	CC (Half)	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	1.83	30	100	0.084	0.084	0.093	0.04	0.999	19.4	5.4		68046		-3	20.4

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	1.83	1.86	100		0.773	0.773	0.857	0.367	0.78	2.2	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7kom	1.83	29.8	64577	3422	99.68	0.1635	0.1619	0.1933	RANDOM	23.732

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]
-1.27			-1.09		2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.694
r_dihedral_angle_4_deg	15.261
r_dihedral_angle_3_deg	9.97
r_dihedral_angle_1_deg	4.426
r_angle_refined_deg	1.364
r_angle_other_deg	0.358
r_chiral_restr	0.062
r_gen_planes_refined	0.056
r_gen_planes_other	0.053
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.694
r_dihedral_angle_4_deg	15.261
r_dihedral_angle_3_deg	9.97
r_dihedral_angle_1_deg	4.426
r_angle_refined_deg	1.364
r_angle_other_deg	0.358
r_chiral_restr	0.062
r_gen_planes_refined	0.056
r_gen_planes_other	0.053
r_bond_refined_d	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4546
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	45

Software

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