5J1D

X-ray crystal structure of Phosphate binding protein (PBP) from Stenotrophomonas maltophilia

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q9T	2Q9T, 2V3Q, 4F1V, 4M1V
experimental model	PDB	2V3Q	2Q9T, 2V3Q, 4F1V, 4M1V
experimental model	PDB	4F1V	2Q9T, 2V3Q, 4F1V, 4M1V
experimental model	PDB	4M1V	2Q9T, 2V3Q, 4F1V, 4M1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.1M Bis-tris, pH 6.5, 20% PEG MME-5000

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.78	α = 90
b = 78.07	β = 102.37
c = 56.38	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	IMAGE PLATE	MARRESEARCH		2011-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	55.071	100	0.08	16.6	4.9		25257

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	1.9	2	100		0.218	3.5	4.7

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	2Q9T, 2V3Q, 4F1V, 4M1V	1.9	55.07	23949	1286	99.98	0.1236	0.1221	0.1512	RANDOM	8.864

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.505
r_dihedral_angle_3_deg	11.274
r_dihedral_angle_4_deg	10.372
r_dihedral_angle_1_deg	6.691
r_angle_refined_deg	1.309
r_angle_other_deg	0.793
r_mcangle_it	0.635
r_mcbond_it	0.378
r_mcbond_other	0.377
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.505
r_dihedral_angle_3_deg	11.274
r_dihedral_angle_4_deg	10.372
r_dihedral_angle_1_deg	6.691
r_angle_refined_deg	1.309
r_angle_other_deg	0.793
r_mcangle_it	0.635
r_mcbond_it	0.378
r_mcbond_other	0.377
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2698
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	17

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
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 R01GM133198.