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WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acrylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PG4 PDB entry 6PG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.16 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.1, 30.1% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.819 α = 90 b = 65.127 β = 90 c = 97.422 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2017-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.54 48.71 97.1 0.999 16.2 13.3 43339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 88 0.847 3.2 12
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 PDB entry 6PG4 1.54 48.71 41119 2165 96.81 0.14917 0.14811 0.1614 0.16952 0.185 RANDOM 15.526
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] 0.2 -1.11 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.858 r_dihedral_angle_4_deg 21.405 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 8.226 r_long_range_B_refined 4.254 r_long_range_B_other 4.032 r_scangle_other 2.51 r_scbond_it 1.615 r_scbond_other 1.593 r_mcangle_it 1.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.858 r_dihedral_angle_4_deg 21.405 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 8.226 r_long_range_B_refined 4.254 r_long_range_B_other 4.032 r_scangle_other 2.51 r_scbond_it 1.615 r_scbond_other 1.593 r_mcangle_it 1.527 r_mcangle_other 1.527 r_angle_refined_deg 1.411 r_angle_other_deg 1.375 r_mcbond_it 0.941 r_mcbond_other 0.941 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2360 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing