3GP3 | pdb_00003gp3

Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	EMERALD CRYO B-4: 100MM MES PH 7.5, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.263	α = 107.96
b = 72.045	β = 93
c = 78.036	γ = 104.2

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2008-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	95.3	0.081	18.062	3.1		149575

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	1.5	1.55	84.9		0.598	1.4	2.1	13280

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	50	148953	7460	94.75	0.238	0.237	0.25	0.268	0.27	RANDOM	19.203

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]
-0.76	-0.12	0.21	0.03	0.53	1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.284
r_dihedral_angle_4_deg	16.972
r_dihedral_angle_3_deg	14.056
r_dihedral_angle_1_deg	6.571
r_scangle_it	5.334
r_scbond_it	3.465
r_mcangle_it	2.266
r_angle_refined_deg	2.114
r_mcbond_it	1.401
r_angle_other_deg	1.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.284
r_dihedral_angle_4_deg	16.972
r_dihedral_angle_3_deg	14.056
r_dihedral_angle_1_deg	6.571
r_scangle_it	5.334
r_scbond_it	3.465
r_mcangle_it	2.266
r_angle_refined_deg	2.114
r_mcbond_it	1.401
r_angle_other_deg	1.099
r_mcbond_other	0.468
r_chiral_restr	0.139
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7298
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	138

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.