6E07

Crystal structure of Canton G6PD in complex with structural NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VFL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M AMMONIUM CITRATE TRIBASIC 20% W/V PEG 3350 0.5 MM AG1, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.12α = 90
b = 206.25β = 90
c = 211.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.650.011000.15310.57.3171050
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)
12.62.741001.4451.57.5

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 REPLACEMENTTHROUGHOUT5VFL2.650.01162393855699.960.18850.187320.21132RANDOM59.785
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]
-0.740.88-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.671
r_dihedral_angle_4_deg19.774
r_dihedral_angle_3_deg16.205
r_dihedral_angle_1_deg6.296
r_long_range_B_refined5.562
r_long_range_B_other5.56
r_scangle_other3.726
r_mcangle_it3.091
r_mcangle_other3.091
r_scbond_it2.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.671
r_dihedral_angle_4_deg19.774
r_dihedral_angle_3_deg16.205
r_dihedral_angle_1_deg6.296
r_long_range_B_refined5.562
r_long_range_B_other5.56
r_scangle_other3.726
r_mcangle_it3.091
r_mcangle_other3.091
r_scbond_it2.32
r_scbond_other2.32
r_mcbond_it1.845
r_mcbond_other1.844
r_angle_refined_deg1.734
r_angle_other_deg0.882
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms31554
Nucleic Acid Atoms
Solvent Atoms537
Heterogen Atoms598

Software

Software
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement