5UKW

Crystal structure of human Glucose 6-phosphate Dehydrogenase mutant (A277C) complexed with G6P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BH9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9291100 mM Tris-HCl pH 9, 200 mM MgCl2, 13% PEG 4000 and 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5351.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.099α = 90
b = 177.817β = 90
c = 216.47γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2014-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97643SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.6546.231000.1540.050.99817.29.216889
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)
12.652.781001.5321.78.8

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 REPLACEMENTTHROUGHOUT2BH92.6546.231604783999.950.191010.188750.23368RANDOM58.671
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]
2.070.24-2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.64
r_dihedral_angle_3_deg20.132
r_dihedral_angle_4_deg18.493
r_long_range_B_refined10.41
r_long_range_B_other10.41
r_scangle_other6.688
r_dihedral_angle_1_deg5.903
r_mcangle_it5.818
r_mcangle_other5.817
r_scbond_it4.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.64
r_dihedral_angle_3_deg20.132
r_dihedral_angle_4_deg18.493
r_long_range_B_refined10.41
r_long_range_B_other10.41
r_scangle_other6.688
r_dihedral_angle_1_deg5.903
r_mcangle_it5.818
r_mcangle_other5.817
r_scbond_it4.273
r_scbond_other4.271
r_mcbond_it3.816
r_mcbond_other3.815
r_angle_other_deg3.595
r_angle_refined_deg1.644
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3862
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing