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WDR5delta32 bound to benzyl (4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.65 α = 90 b = 65.204 β = 90 c = 97.477 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 2016-04-28 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 1.99 48.74 98.5 0.998 17.2 7.3 20794
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 1.99 2.04 95 0.946 5.8 7.2
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 6PG4 1.99 42.11 19707 1049 98.23 0.15898 0.15674 0.1661 0.20159 0.2092 RANDOM 12.663
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] 0.02 -0.93 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.454 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 8.24 r_long_range_B_refined 3.898 r_long_range_B_other 3.897 r_angle_other_deg 2.374 r_scangle_other 1.897 r_angle_refined_deg 1.395 r_mcangle_it 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.454 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 8.24 r_long_range_B_refined 3.898 r_long_range_B_other 3.897 r_angle_other_deg 2.374 r_scangle_other 1.897 r_angle_refined_deg 1.395 r_mcangle_it 1.27 r_mcangle_other 1.27 r_scbond_it 1.174 r_scbond_other 1.15 r_mcbond_it 0.77 r_mcbond_other 0.769 r_chiral_restr 0.063 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 278 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing