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Crystal structure of human WDR5 in complex with compound 9o
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% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.939 α = 107.17 b = 54.779 β = 90.21 c = 64.011 γ = 112.61
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 MX-300 2012-01-25 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) Rrim I (All) Rpim I (All) 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 1.8 50 96.5 0.105 0.126 0.068 7.3 3.2 50164
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) Redundancy Number Unique Reflections (All) 1 1.8 1.83 77.9 0.437 0.533 0.3 0.793 3 2029
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 1.8 50 48908 1042 96.67 0.1973 0.1967 0.1977 0.2279 0.2327 RANDOM 20.624
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] -0.7 0.8 -0.05 1.27 0.4 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 23.85 r_dihedral_angle_3_deg 14.143 r_dihedral_angle_1_deg 7.431 r_angle_refined_deg 1.417 r_mcangle_it 1.387 r_scbond_it 1.128 r_mcbond_it 0.896 r_chiral_restr 0.09 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 23.85 r_dihedral_angle_3_deg 14.143 r_dihedral_angle_1_deg 7.431 r_angle_refined_deg 1.417 r_mcangle_it 1.387 r_scbond_it 1.128 r_mcbond_it 0.896 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4676 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 128
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing HKL-3000 data reduction