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Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 23% PEG3350, 0.2N ammonium acetate, 0.1M Bis-tris pH5.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.82 α = 90 b = 59.857 β = 93.73 c = 102.011 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 X 6M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.88 50 98 0.065 0.071 0.03 5.5 5.4 73841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 93.8 0.735 0.815 0.343 0.869 4.9
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 6BW3 1.88 46.99 72452 699 98.12 0.184 0.1836 0.1915 0.2357 0.2492 RANDOM 38.944
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] 4.2 -0.25 -3.37 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.236 r_dihedral_angle_4_deg 17.352 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 7.93 r_angle_refined_deg 1.38 r_angle_other_deg 1.276 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.236 r_dihedral_angle_4_deg 17.352 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 7.93 r_angle_refined_deg 1.38 r_angle_other_deg 1.276 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6041 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction HKL-3000 data reduction