7M2O

Crystal structure of Human Glycolate Oxidase with Inhibitor Compound 15


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M Tris-HCL pH 8.5, 25 % (w/v) PEG 1000
Crystal Properties
Matthews coefficientSolvent content
2.1943.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.904α = 90
b = 96.904β = 90
c = 79.536γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2019-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.075099.90.09514.6622486
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.110.797

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 REPLACEMENTTHROUGHOUT2RDW2.0739.7721419106599.810.127930.125970.16607RANDOM21.264
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.04
r_dihedral_angle_4_deg18.1
r_dihedral_angle_3_deg14.858
r_long_range_B_refined7.453
r_long_range_B_other7.453
r_dihedral_angle_1_deg6.649
r_scangle_other4.405
r_scbond_it2.901
r_scbond_other2.9
r_mcangle_it2.395
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.04
r_dihedral_angle_4_deg18.1
r_dihedral_angle_3_deg14.858
r_long_range_B_refined7.453
r_long_range_B_other7.453
r_dihedral_angle_1_deg6.649
r_scangle_other4.405
r_scbond_it2.901
r_scbond_other2.9
r_mcangle_it2.395
r_mcangle_other2.395
r_angle_refined_deg1.754
r_mcbond_it1.727
r_mcbond_other1.726
r_angle_other_deg1.365
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms2602
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing