5J1D

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

X-RAY DIFFRACTION

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.