2WF5

Structure of Beta-Phosphoglucomutase inhibited with Glucose-6-phosphate and trifluoromagnesate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O08PDB ENTRY 1O08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.219-21 % PEG 3350 AND 50 MM MG ACETATE, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.0138.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.647α = 90
b = 54.659β = 90
c = 105.12γ = 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
11.32084.80.068.52.5455203
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)
11.31.3747.20.242.71.8

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 1O081.32043252225683.980.17360.172620.19173RANDOM10.212
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]
1.13-1.230.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.781
r_dihedral_angle_4_deg19.47
r_dihedral_angle_3_deg12.409
r_dihedral_angle_1_deg5.886
r_sphericity_free4.919
r_scangle_it3.545
r_sphericity_bonded2.511
r_scbond_it2.27
r_angle_refined_deg1.501
r_mcangle_it1.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.781
r_dihedral_angle_4_deg19.47
r_dihedral_angle_3_deg12.409
r_dihedral_angle_1_deg5.886
r_sphericity_free4.919
r_scangle_it3.545
r_sphericity_bonded2.511
r_scbond_it2.27
r_angle_refined_deg1.501
r_mcangle_it1.469
r_angle_other_deg1.059
r_rigid_bond_restr1.025
r_mcbond_it0.916
r_mcbond_other0.415
r_chiral_restr0.205
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
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 Atoms202
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing