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WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide
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 0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.366 α = 90 b = 46.974 β = 112.75 c = 129.274 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 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 1.68 43.74 99 0.999 17.5 7.4 70355
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 1.68 1.71 94.6 0.834 2.7 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 6PG3 1.68 43.74 66909 3444 99.04 0.16684 0.16549 0.1758 0.19337 0.2032 RANDOM 17.336
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] 0.98 0.2 0.57 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 24.203 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 7.983 r_long_range_B_refined 4.458 r_long_range_B_other 4.458 r_scangle_other 2.583 r_angle_other_deg 2.338 r_mcangle_it 1.946 r_mcangle_other 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 24.203 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 7.983 r_long_range_B_refined 4.458 r_long_range_B_other 4.458 r_scangle_other 2.583 r_angle_other_deg 2.338 r_mcangle_it 1.946 r_mcangle_other 1.946 r_scbond_it 1.603 r_scbond_other 1.603 r_angle_refined_deg 1.423 r_mcbond_it 1.195 r_mcbond_other 1.194 r_chiral_restr 0.07 r_bond_other_d 0.036 r_bond_refined_d 0.01 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 4690 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing