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Crystal structure of human WDR5 in complex with compound 9d
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 5.5 291 22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.64 α = 107.92 b = 53.615 β = 90.95 c = 64.707 γ = 109.66
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 94.1 0.042 17 4 48569
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 89.8 0.207 4 2295
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 47564 1005 93.86 0.1534 0.1527 0.153 0.185 0.1849 RANDOM 19.754
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] -0.39 0.25 -0.55 0.98 0.1 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.009 r_dihedral_angle_4_deg 19.389 r_dihedral_angle_3_deg 12.585 r_dihedral_angle_1_deg 7.383 r_angle_refined_deg 1.394 r_mcangle_it 1.337 r_scbond_it 1.246 r_mcbond_it 0.859 r_chiral_restr 0.089 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.009 r_dihedral_angle_4_deg 19.389 r_dihedral_angle_3_deg 12.585 r_dihedral_angle_1_deg 7.383 r_angle_refined_deg 1.394 r_mcangle_it 1.337 r_scbond_it 1.246 r_mcbond_it 0.859 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 4615 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 149
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing