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Crystal structure of human WDR5 in complex with L-arginine
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, 0.66 mM L-arginine
Crystal Properties Matthews coefficient Solvent content 2.1 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.186 α = 90 b = 86.703 β = 90 c = 40.963 γ = 90
Symmetry Space Group P 21 21 2
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 mirror 2018-10-24 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 1.92 59.26 99 0.04 10.7 12.5 22592
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 1.92 1.97 84.7 0.29 3.1 10.9
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 1.92 59.26 21429 1117 98.9 0.16203 0.15989 0.1729 0.20068 0.2092 RANDOM 25.994
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] -1.81 -1.21 3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 16.77 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_1_deg 7.689 r_long_range_B_refined 5.423 r_long_range_B_other 5.423 r_scangle_other 3.225 r_mcangle_it 2.087 r_mcangle_other 2.087 r_scbond_it 2.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 16.77 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_1_deg 7.689 r_long_range_B_refined 5.423 r_long_range_B_other 5.423 r_scangle_other 3.225 r_mcangle_it 2.087 r_mcangle_other 2.087 r_scbond_it 2.057 r_scbond_other 2.057 r_angle_refined_deg 1.449 r_mcbond_it 1.37 r_mcbond_other 1.37 r_angle_other_deg 0.905 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing