6A7X

Rat Xanthine oxidoreductase, D428A variant, NAD bound form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293PEG 8000, HEPES, lithium sulfate, pH 6.2
Crystal Properties
Matthews coefficientSolvent content
2.5652.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.135α = 90
b = 137.792β = 90
c = 222.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1541.6399.41.721.72306011
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1541.63

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 DIFFRACTIONTHROUGHOUT2.1541.63154557817199.390.198070.19510.25488RANDOM40.59
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.519
r_long_range_B_refined21.419
r_long_range_B_other20.75
r_dihedral_angle_4_deg17.761
r_dihedral_angle_3_deg15.373
r_dihedral_angle_1_deg7.171
r_scangle_other4.682
r_mcangle_it3.814
r_mcangle_other3.814
r_scbond_it3.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.519
r_long_range_B_refined21.419
r_long_range_B_other20.75
r_dihedral_angle_4_deg17.761
r_dihedral_angle_3_deg15.373
r_dihedral_angle_1_deg7.171
r_scangle_other4.682
r_mcangle_it3.814
r_mcangle_other3.814
r_scbond_it3.073
r_scbond_other3.073
r_mcbond_it2.568
r_mcbond_other2.568
r_angle_refined_deg1.339
r_angle_other_deg0.874
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms19981
Nucleic Acid Atoms
Solvent Atoms1593
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing