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WDR5delta32 bound to (2-(3-methoxy-3-phenylpropyl)-1H-imidazol-4-yl)methanol
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 0.17 M ammonium sulfate, 0.1 bis-tris chloride (pH 6.3), 30.5 %w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.963 α = 90 b = 65.303 β = 90 c = 97.307 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 2016-07-09 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 2.45 48.65 99.7 0.997 13.1 6.9 11523
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 2.45 2.55 97.6 0.808 2.4 6.8
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 6PG4 2.45 48.65 10945 536 99.67 0.19791 0.19559 0.2011 0.24305 0.2511 RANDOM 37.873
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] 3.5 -4.48 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.168 r_dihedral_angle_4_deg 25.902 r_dihedral_angle_3_deg 14.803 r_dihedral_angle_1_deg 8.264 r_long_range_B_refined 6.809 r_long_range_B_other 6.809 r_scangle_other 3.505 r_mcangle_it 3.309 r_mcangle_other 3.308 r_angle_other_deg 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.168 r_dihedral_angle_4_deg 25.902 r_dihedral_angle_3_deg 14.803 r_dihedral_angle_1_deg 8.264 r_long_range_B_refined 6.809 r_long_range_B_other 6.809 r_scangle_other 3.505 r_mcangle_it 3.309 r_mcangle_other 3.308 r_angle_other_deg 2.344 r_scbond_it 2.154 r_scbond_other 2.153 r_mcbond_it 2.059 r_mcbond_other 2.056 r_angle_refined_deg 1.403 r_chiral_restr 0.06 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_other 0.007 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 2360 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing