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Crystal structure of human WDR5 in complex with compound 9h
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 20% PEG 5K MME, 0.1 M BisTris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.191 α = 110.67 b = 60.962 β = 90.43 c = 64.126 γ = 109.47
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2012-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.8 50 94.2 0.071 9.5 3.9 54564
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 1.8 1.83 90.5 0.618 4 2635
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 53391 1125 94.17 0.1792 0.1785 0.1791 0.2106 0.2121 RANDOM 23.039
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] -0.04 0.72 0.14 1.06 0.16 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 17.181 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 7.367 r_mcangle_it 1.672 r_angle_refined_deg 1.378 r_scbond_it 1.237 r_mcbond_it 1.082 r_chiral_restr 0.089 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 17.181 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 7.367 r_mcangle_it 1.672 r_angle_refined_deg 1.378 r_scbond_it 1.237 r_mcbond_it 1.082 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 165
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing HKL-2000 data reduction