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Crystal structure of human WDR5 in complex with monomethyl H3R2 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 295 100 mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 1.67 mM monomethyl H3R2 peptide
Crystal Properties Matthews coefficient Solvent content 2.27 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.294 α = 90 b = 98.632 β = 90 c = 80.265 γ = 90
Symmetry Space Group C 2 2 21
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 MX225HE KB mirrors 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.66 61.32 100 0.07 8.2 7.1 37045
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 100 0.34 2 7.4
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 2H14 1.66 61.32 35159 1862 99.94 0.1731 0.1715 0.1814 0.2018 0.2088 RANDOM 14.841
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] -0.4 1.08 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.141 r_dihedral_angle_4_deg 19.374 r_dihedral_angle_3_deg 12.481 r_dihedral_angle_1_deg 7.537 r_angle_refined_deg 1.453 r_angle_other_deg 1.046 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.141 r_dihedral_angle_4_deg 19.374 r_dihedral_angle_3_deg 12.481 r_dihedral_angle_1_deg 7.537 r_angle_refined_deg 1.453 r_angle_other_deg 1.046 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2382 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing