7KP2

High Resolution Crystal Structure of Putative Pterin Binding Protein (PruR) from Vibrio cholerae O1 biovar El Tor str. N16961 in Complex with Neopterin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 8.8 mg/ml, 0.01M Tris pH 8.3, 2mM Neopterin; Screen: Classics II (D11), 0.1M Bis-Tris pH 6.5, 28% (w/v) PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.488	α = 90
b = 54.616	β = 91.5
c = 33.448	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	100	CCD	MARMOSAIC 300 mm CCD	Be	2019-07-24	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)	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	1.03	30	96.5	0.092	0.092	0.105	0.049	22.1	4.6		57114		-3	7.9

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	1.03	1.05	93.4		0.764	0.764	0.867	0.404	0.719	3.2	4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.03	21.48	54176	2929	96.3	0.1286	0.1276	0.1467	RANDOM	10.534

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]
0.13		-0.08	-0.52		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	8.219
r_dihedral_angle_1_deg	4.794
r_dihedral_angle_2_deg	3.718
r_rigid_bond_restr	2.135
r_angle_refined_deg	1.271
r_angle_other_deg	0.417
r_chiral_restr	0.065
r_gen_planes_refined	0.019
r_gen_planes_other	0.018
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	8.219
r_dihedral_angle_1_deg	4.794
r_dihedral_angle_2_deg	3.718
r_rigid_bond_restr	2.135
r_angle_refined_deg	1.271
r_angle_other_deg	0.417
r_chiral_restr	0.065
r_gen_planes_refined	0.019
r_gen_planes_other	0.018
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1096
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	36

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 National Science Foundation (DBI-1832184), 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 R01GM133198.