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Crystal structure of human WDR5 in complex with compound 9e
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 28% PEG 2K MME, 0.1 M BisTris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.162 α = 90 b = 48.232 β = 108.01 c = 63.448 γ = 90
Symmetry Space Group C 1 2 1
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 0.97931 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 1.73 50 99.2 0.079 9.4 4.1 29229
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 1.73 1.76 92.5 0.452 3.6 1352
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 1.73 50 28135 940 99 0.2057 0.2045 0.2047 0.2409 0.2387 RANDOM 27.325
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] 3.48 -0.03 -1.65 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.706 r_dihedral_angle_4_deg 23.631 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 7.092 r_mcangle_it 2.215 r_scbond_it 1.553 r_mcbond_it 1.422 r_angle_refined_deg 1.421 r_chiral_restr 0.091 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.706 r_dihedral_angle_4_deg 23.631 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 7.092 r_mcangle_it 2.215 r_scbond_it 1.553 r_mcbond_it 1.422 r_angle_refined_deg 1.421 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 73
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing