6W45

Crystal structure of HAO1 in complex with biaryl acid inhibitor - compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GMB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M TRIS.HCl pH 8.5, 25 %(v/v) PEG 550 MME
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.27α = 90
b = 97.27β = 90
c = 80.458γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11.03923SSRFBL19U1

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
11.738.399.70.05934.98.941345
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)
11.71.731000.4235.99

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 REPLACEMENTTHROUGHOUT6GMB1.738.339275206999.580.1490.1470.1864RANDOM25.681
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]
-0.55-0.551.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.529
r_dihedral_angle_4_deg15.763
r_dihedral_angle_3_deg13.486
r_dihedral_angle_1_deg6.112
r_angle_refined_deg1.743
r_angle_other_deg1.483
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.529
r_dihedral_angle_4_deg15.763
r_dihedral_angle_3_deg13.486
r_dihedral_angle_1_deg6.112
r_angle_refined_deg1.743
r_angle_other_deg1.483
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2520
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling