2WF8

Structure of Beta-Phosphoglucomutase inhibited with Glucose-6- phosphate, Glucose-1-phosphate and Beryllium trifluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WF5PDB ENTRY 2WF5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528-29 % PEG 4000 AND 200 MM NA ACETATE, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.831.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.3α = 90
b = 54.3β = 90
c = 104.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGE211MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.22092.30.0418.44.461544311.3
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)
11.21.2666.90.382.73.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WF51.22058366312191.80.1630.1620.191RANDOM11.6
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]
1.11-0.89-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.652
r_dihedral_angle_4_deg19.666
r_dihedral_angle_3_deg12.144
r_sphericity_free5.578
r_dihedral_angle_1_deg5.002
r_sphericity_bonded3.947
r_scangle_it3.554
r_scbond_it2.337
r_mcangle_it1.65
r_angle_refined_deg1.627
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.652
r_dihedral_angle_4_deg19.666
r_dihedral_angle_3_deg12.144
r_sphericity_free5.578
r_dihedral_angle_1_deg5.002
r_sphericity_bonded3.947
r_scangle_it3.554
r_scbond_it2.337
r_mcangle_it1.65
r_angle_refined_deg1.627
r_rigid_bond_restr1.115
r_mcbond_it1.072
r_angle_other_deg0.877
r_mcbond_other0.632
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1680
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing