8QYT

Human Pyridoxine-5'-phosphate oxidase in complex with PLP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NRG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29312% vv PEG 6000, 0.1M Sodium Citrate, 0.1M Lithium Sulfate
Crystal Properties
Matthews coefficientSolvent content
1.9436.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.48α = 90
b = 82.48β = 90
c = 59.19γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.000ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.6945.61000.05130.218.426324
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)
11.691.721.4430.8418.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6945.624998132699.970.175050.172850.21563RANDOM34.046
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]
-0.31-0.16-0.311.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.793
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg14.962
r_long_range_B_other7.227
r_long_range_B_refined7.212
r_dihedral_angle_1_deg7.049
r_scangle_other5.858
r_scbond_other4.044
r_scbond_it4.039
r_mcangle_other3.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.793
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg14.962
r_long_range_B_other7.227
r_long_range_B_refined7.212
r_dihedral_angle_1_deg7.049
r_scangle_other5.858
r_scbond_other4.044
r_scbond_it4.039
r_mcangle_other3.69
r_mcangle_it3.687
r_mcbond_it2.816
r_mcbond_other2.803
r_angle_refined_deg1.664
r_angle_other_deg1.375
r_chiral_restr0.082
r_bond_refined_d0.011
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 Atoms1714
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing