2WF9

Structure of Beta-Phosphoglucomutase inhibited with Glucose-6- phosphate, and Beryllium trifluoride, crystal form 2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.228-29 % PEG 4000 AND 200 MM NA ACETATE, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
1.7553

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.1α = 90
b = 72.7β = 90
c = 85.2γ = 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
11.42090.20.0514.22.935943311.8
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)
11.41.4858.50.292.42.4

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 2WF51.42034083181489.50.1850.1840.2RANDOM10.35
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]
-0.12-0.040.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.456
r_dihedral_angle_3_deg12.535
r_dihedral_angle_4_deg11.021
r_dihedral_angle_1_deg6.722
r_scangle_it2.449
r_scbond_it2.422
r_rigid_bond_restr1.998
r_angle_refined_deg1.65
r_sphericity_free1.631
r_sphericity_bonded0.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.456
r_dihedral_angle_3_deg12.535
r_dihedral_angle_4_deg11.021
r_dihedral_angle_1_deg6.722
r_scangle_it2.449
r_scbond_it2.422
r_rigid_bond_restr1.998
r_angle_refined_deg1.65
r_sphericity_free1.631
r_sphericity_bonded0.958
r_mcangle_it0.909
r_angle_other_deg0.901
r_mcbond_it0.492
r_mcbond_other0.112
r_chiral_restr0.066
r_gen_planes_refined0.016
r_bond_refined_d0.014
r_bond_other_d0.008
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 Atoms1708
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing