5QID

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1787627869


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
Matthews coefficientSolvent content
2.3447.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.487α = 90
b = 97.487β = 90
c = 80.388γ = 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
11.4526.1699.90.0540.0590.0230.99917.45.966577
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)
11.451.4998.70.5670.6620.3360.7823.84830

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 SYNTHESISTHROUGHOUT2NZL1.4568.9363175340099.880.18060.17970.1975RANDOM19.904
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]
-0.6-0.61.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.273
r_dihedral_angle_4_deg14.841
r_dihedral_angle_3_deg13.091
r_dihedral_angle_1_deg6.456
r_mcangle_it2.102
r_angle_refined_deg1.809
r_mcbond_it1.369
r_mcbond_other1.369
r_angle_other_deg1.009
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.273
r_dihedral_angle_4_deg14.841
r_dihedral_angle_3_deg13.091
r_dihedral_angle_1_deg6.456
r_mcangle_it2.102
r_angle_refined_deg1.809
r_mcbond_it1.369
r_mcbond_other1.369
r_angle_other_deg1.009
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2608
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing