3ZI4

The structure of Beta-phosphoglucomutase Inhibited With Glucose-6-phosphate and Scandium Tetrafluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WF6PDB ENTRY 2WF6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.219-21 % PEG 4000 AND 50 MM NAAC, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.1743.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.152α = 90
b = 54.238β = 90
c = 104.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGALLIUM2212009-11-20MSINGLE WAVELENGTH
21x-ray100CCDADSC CCDM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1
2SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.3320940.0518.73.4461713
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)
11.331.476.60.452.43

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 2WF61.332043810233193.360.132370.130180.17379RANDOM13.298
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]
0.8-0.930.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_sphericity_free23.225
r_dihedral_angle_4_deg19.201
r_dihedral_angle_3_deg11.543
r_sphericity_bonded6.859
r_dihedral_angle_1_deg5.328
r_rigid_bond_restr3.911
r_angle_refined_deg1.676
r_angle_other_deg0.864
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_sphericity_free23.225
r_dihedral_angle_4_deg19.201
r_dihedral_angle_3_deg11.543
r_sphericity_bonded6.859
r_dihedral_angle_1_deg5.328
r_rigid_bond_restr3.911
r_angle_refined_deg1.676
r_angle_other_deg0.864
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.011
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms422
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing