4QL1

Crystal structure of human WDR5 in complex with compound OICR-9429


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UR4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529125% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.843α = 71.45
b = 56.628β = 88.94
c = 64.688γ = 65.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
11.55094.80.06739.53.7858289.8
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)
11.51.5370.20.3923.73202

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 REPLACEMENTTHROUGHOUT3UR41.55085825169594.450.1960.19540.2266RANDOM15.328
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]
0.31-0.12-0.20.410.01-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.798
r_dihedral_angle_4_deg21.038
r_dihedral_angle_3_deg12.087
r_dihedral_angle_1_deg7.36
r_mcangle_it1.445
r_angle_refined_deg1.373
r_mcbond_it0.858
r_mcbond_other0.858
r_angle_other_deg0.826
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.798
r_dihedral_angle_4_deg21.038
r_dihedral_angle_3_deg12.087
r_dihedral_angle_1_deg7.36
r_mcangle_it1.445
r_angle_refined_deg1.373
r_mcbond_it0.858
r_mcbond_other0.858
r_angle_other_deg0.826
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4620
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms84

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building