5QIG

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1407672867


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.752930.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Crystal Properties
Matthew coefficientSolvent content
2.3547.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.54α = 90
b = 97.54β = 90
c = 80.646γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-01-29SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.4226.2199.80.0450.0490.0190.99919.15.771180
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.4698.50.5510.650.340.7543.55192

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2NZL1.4268.9767577359799.840.1570.15540.1868RANDOM19.117
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]
-0.66-0.661.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.259
r_dihedral_angle_4_deg13.928
r_sphericity_free13.621
r_dihedral_angle_3_deg12.377
r_sphericity_bonded7.5
r_dihedral_angle_1_deg6.163
r_mcangle_it2.512
r_rigid_bond_restr2.286
r_mcbond_it2.014
r_mcbond_other1.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.259
r_dihedral_angle_4_deg13.928
r_sphericity_free13.621
r_dihedral_angle_3_deg12.377
r_sphericity_bonded7.5
r_dihedral_angle_1_deg6.163
r_mcangle_it2.512
r_rigid_bond_restr2.286
r_mcbond_it2.014
r_mcbond_other1.997
r_angle_refined_deg1.65
r_angle_other_deg1.042
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2715
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing