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WDR5delta32 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)-2-phenylacetamide
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 0.101 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.63, 25.8% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.798 α = 90 b = 65.275 β = 90 c = 97.127 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 CCD ADSC QUANTUM 315r 2016-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 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 1.73 48.56 98.1 0.996 12.6 13.6 31184
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 1.73 1.76 80 0.862 2.8
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 1.73 48.56 29595 1534 97.86 0.17612 0.174 0.1845 0.21697 0.2276 RANDOM 10.552
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] -0.71 -0.79 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.48 r_dihedral_angle_4_deg 22.107 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 8.575 r_long_range_B_refined 4.47 r_long_range_B_other 4.469 r_angle_other_deg 2.35 r_scangle_other 1.578 r_angle_refined_deg 1.407 r_mcangle_it 1.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.48 r_dihedral_angle_4_deg 22.107 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 8.575 r_long_range_B_refined 4.47 r_long_range_B_other 4.469 r_angle_other_deg 2.35 r_scangle_other 1.578 r_angle_refined_deg 1.407 r_mcangle_it 1.331 r_mcangle_other 1.33 r_scbond_it 0.974 r_scbond_other 0.947 r_mcbond_it 0.764 r_mcbond_other 0.763 r_chiral_restr 0.065 r_bond_other_d 0.036 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 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 352 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing