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WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.915 α = 110.56 b = 61.493 β = 91.06 c = 64.757 γ = 112.38
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 2016-08-16 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 1.75 52.42 99.9 0.97 4.4 3.7 62036
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 1.75 1.79 100 0.781 2 3.8
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 6PG3 1.75 52.42 59026 3005 99.84 0.23435 0.23263 0.2386 0.26877 0.2718 RANDOM 12.722
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] 0.34 0.26 -0.27 1.03 -0.17 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.39 r_dihedral_angle_4_deg 16.127 r_dihedral_angle_3_deg 13.919 r_dihedral_angle_1_deg 8.474 r_long_range_B_refined 3.822 r_long_range_B_other 3.821 r_angle_other_deg 2.36 r_mcangle_it 1.778 r_mcangle_other 1.778 r_scangle_other 1.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.39 r_dihedral_angle_4_deg 16.127 r_dihedral_angle_3_deg 13.919 r_dihedral_angle_1_deg 8.474 r_long_range_B_refined 3.822 r_long_range_B_other 3.821 r_angle_other_deg 2.36 r_mcangle_it 1.778 r_mcangle_other 1.778 r_scangle_other 1.594 r_angle_refined_deg 1.43 r_mcbond_it 1.017 r_mcbond_other 1.016 r_scbond_it 0.955 r_scbond_other 0.954 r_chiral_restr 0.062 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 4714 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing