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WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol
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 0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.118 α = 104.7 b = 75.831 β = 96.41 c = 79.239 γ = 105.23
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 2016-07-09 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 1.67 46.71 96.4 0.999 11.3 3.8 128452
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 1.67 1.7 92.1 0.751 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 1.67 46.71 122246 6204 96.41 0.18782 0.18683 0.1945 0.20678 0.2129 RANDOM 19.039
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] 0.29 -0.5 0.12 -0.61 0.21 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 17.752 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 8.086 r_long_range_B_refined 4.305 r_long_range_B_other 4.305 r_scangle_other 2.833 r_angle_other_deg 2.345 r_mcangle_other 2.006 r_mcangle_it 2.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 17.752 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 8.086 r_long_range_B_refined 4.305 r_long_range_B_other 4.305 r_scangle_other 2.833 r_angle_other_deg 2.345 r_mcangle_other 2.006 r_mcangle_it 2.005 r_scbond_it 1.789 r_scbond_other 1.786 r_angle_refined_deg 1.407 r_mcbond_it 1.328 r_mcbond_other 1.326 r_chiral_restr 0.07 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 9419 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing