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WDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate
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 0.237 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.92, 25.7% w/v MPEG5000
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.716 α = 90 b = 65.285 β = 90 c = 97.173 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 1.81 46.72 99.2 0.999 17.1 7.2 27580
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 1.81 1.85 87 0.791 2.6 7.1
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 1.81 42.14 26139 1383 99.7 0.20529 0.20302 0.2089 0.2477 0.2492 RANDOM 21.431
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] -0.16 -1.47 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.968 r_dihedral_angle_4_deg 25.764 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 8.09 r_long_range_B_refined 3.864 r_long_range_B_other 3.864 r_scangle_other 2.423 r_angle_other_deg 2.354 r_mcangle_it 2.153 r_mcangle_other 2.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.968 r_dihedral_angle_4_deg 25.764 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 8.09 r_long_range_B_refined 3.864 r_long_range_B_other 3.864 r_scangle_other 2.423 r_angle_other_deg 2.354 r_mcangle_it 2.153 r_mcangle_other 2.152 r_scbond_it 1.557 r_scbond_other 1.556 r_angle_refined_deg 1.437 r_mcbond_it 1.382 r_mcbond_other 1.382 r_chiral_restr 0.061 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 200 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing