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Crystal structure of human WDR5 in complex with compound OICR-9429
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.843 α = 71.45 b = 56.628 β = 88.94 c = 64.688 γ = 65.43
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2013-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 50 94.8 0.067 39.5 3.7 85828 9.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 70.2 0.392 3.7 3202
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UR4 1.5 50 85825 1695 94.45 0.196 0.1954 0.2032 0.2266 0.2284 RANDOM 15.328
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 -0.2 0.41 0.01 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.798 r_dihedral_angle_4_deg 21.038 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 7.36 r_mcangle_it 1.445 r_angle_refined_deg 1.373 r_mcbond_it 0.858 r_mcbond_other 0.858 r_angle_other_deg 0.826 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.798 r_dihedral_angle_4_deg 21.038 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 7.36 r_mcangle_it 1.445 r_angle_refined_deg 1.373 r_mcbond_it 0.858 r_mcbond_other 0.858 r_angle_other_deg 0.826 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4620 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 84
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MxDC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building