☰ Navigation Tabs
WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.825 α = 90 b = 46.85 β = 112.81 c = 129.154 γ = 90
Symmetry Space Group I 1 2 1
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 2015-08-18 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 2.04 43.63 99.6 0.994 10.3 7.4 39721
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 2.04 2.1 94.8 0.866 2.7 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 2H9L 2.04 43.63 37833 1887 99.57 0.17459 0.173 0.1804 0.20617 0.2104 RANDOM 17.693
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] 1.94 0.1 0.04 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.762 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 8.263 r_long_range_B_refined 4.119 r_long_range_B_other 4.119 r_scangle_other 2.573 r_angle_other_deg 2.339 r_mcangle_it 1.807 r_mcangle_other 1.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.762 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 8.263 r_long_range_B_refined 4.119 r_long_range_B_other 4.119 r_scangle_other 2.573 r_angle_other_deg 2.339 r_mcangle_it 1.807 r_mcangle_other 1.806 r_scbond_it 1.577 r_scbond_other 1.577 r_angle_refined_deg 1.392 r_mcbond_it 1.123 r_mcbond_other 1.122 r_chiral_restr 0.06 r_bond_other_d 0.036 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 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 4650 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing