7ZVD

K89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a complex with structural NADP+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1M Hepes pH 7.2, 0.2M L-Proline, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.22α = 90
b = 172.22β = 90
c = 216.48γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.4654.9899.90.032910.046540.0329113.21220737
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.540.6840.588

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 REPLACEMENTTHROUGHOUT6E082.4654.9819700103699.890.211780.207660.28934RANDOM63.226
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]
2.592.52-5.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.515
r_dihedral_angle_2_deg17.769
r_long_range_B_refined11.389
r_long_range_B_other11.388
r_scangle_other9.64
r_dihedral_angle_1_deg9.439
r_mcangle_other7.809
r_mcangle_it7.808
r_scbond_it6.89
r_scbond_other6.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.515
r_dihedral_angle_2_deg17.769
r_long_range_B_refined11.389
r_long_range_B_other11.388
r_scangle_other9.64
r_dihedral_angle_1_deg9.439
r_mcangle_other7.809
r_mcangle_it7.808
r_scbond_it6.89
r_scbond_other6.886
r_mcbond_it5.86
r_mcbond_other5.839
r_angle_refined_deg2.03
r_angle_other_deg0.777
r_chiral_restr0.103
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.008
r_gen_planes_other0.004
r_dihedral_angle_4_deg
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 Atoms3980
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing