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Crystal structure of human BRD9 bromodomain in complex with a PROTAC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 24% PEG 3350
0.2 M NH4F
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.84 α = 90 b = 59.82 β = 108.75 c = 60.34 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 PILATUS 6M-F 2017-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 41.3 98.5 0.084 0.096 0.046 0.99 18.9 4.2 10196
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 2.4 2.49 99.9 0.157 0.178 0.084 0.98 4.3
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 5I40 2.4 41.3 9627 556 98.34 0.2177 0.2158 0.2163 0.2507 0.2494 RANDOM 22.469
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] -0.88 -0.5 2.39 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 16.033 r_dihedral_angle_3_deg 15.913 r_dihedral_angle_1_deg 4.422 r_angle_refined_deg 1.202 r_angle_other_deg 0.82 r_chiral_restr 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 16.033 r_dihedral_angle_3_deg 15.913 r_dihedral_angle_1_deg 4.422 r_angle_refined_deg 1.202 r_angle_other_deg 0.82 r_chiral_restr 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1826 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 66
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction