6E08

Crystal structure of G6PD in complex with structural NADP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.329320% w/v PEG 3350, 0.2 M potassium formate
Crystal Properties
Matthews coefficientSolvent content
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.58α = 90
b = 173.41β = 90
c = 215.909γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.0SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.95095.30.791115.740413
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9591.30.120.8235.7

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 REPLACEMENTTHROUGHOUT2BHL1.918.2840413217194.690.174020.171820.21258RANDOM24.422
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]
0.010.04-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg14.464
r_dihedral_angle_1_deg6.852
r_long_range_B_refined5.464
r_long_range_B_other5.382
r_scangle_other3.906
r_scbond_it2.453
r_scbond_other2.453
r_mcangle_it2.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg14.464
r_dihedral_angle_1_deg6.852
r_long_range_B_refined5.464
r_long_range_B_other5.382
r_scangle_other3.906
r_scbond_it2.453
r_scbond_other2.453
r_mcangle_it2.147
r_mcangle_other2.146
r_angle_refined_deg1.786
r_mcbond_it1.427
r_mcbond_other1.426
r_angle_other_deg1.07
r_chiral_restr0.099
r_bond_refined_d0.015
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3946
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing