3GW8

Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with vanadate and glycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EZN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6289Emerald Cryo Screen B-4, 100 mM MES pH 6.0, 5% PEG 1000, 10% glycerol, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1843.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.175α = 106.42
b = 49.112β = 91.18
c = 62.59γ = 107.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.935092.80.06621.9753.434058
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.93280.40.3012.892.22972

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3EZN1.935034057169692.620.1890.1870.227RANDOM22.537
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]
0.580.31-0.28-0.380.170.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.778
r_dihedral_angle_4_deg18.038
r_dihedral_angle_3_deg12.783
r_dihedral_angle_1_deg6.004
r_scangle_it2.505
r_scbond_it1.511
r_angle_refined_deg1.2
r_mcangle_it1.019
r_angle_other_deg0.838
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.778
r_dihedral_angle_4_deg18.038
r_dihedral_angle_3_deg12.783
r_dihedral_angle_1_deg6.004
r_scangle_it2.505
r_scbond_it1.511
r_angle_refined_deg1.2
r_mcangle_it1.019
r_angle_other_deg0.838
r_mcbond_it0.55
r_mcbond_other0.115
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3666
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms82

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling