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Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277.15 0.1M MMT pH6, 30% PEG 1k
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.015 α = 90 b = 29.458 β = 92.24 c = 141.187 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 PIXEL DECTRIS PILATUS 6M 2013-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9795 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.95 28.84 98.3 0.033 0.032 20.3 3.2 18127 18127
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 97.9 0.123 6.1 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 3HME 1.95 28.84 17121 923 97.67 0.18372 0.18118 0.1888 0.22989 0.2335 RANDOM 30.104
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] -0.8 0.7 2.26 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_3_deg 14.371 r_dihedral_angle_4_deg 12.165 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 5.486 r_long_range_B_other 5.443 r_scangle_other 4.094 r_scbond_it 2.632 r_scbond_other 2.631 r_mcangle_it 2.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_3_deg 14.371 r_dihedral_angle_4_deg 12.165 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 5.486 r_long_range_B_other 5.443 r_scangle_other 4.094 r_scbond_it 2.632 r_scbond_other 2.631 r_mcangle_it 2.293 r_mcangle_other 2.293 r_angle_refined_deg 2.069 r_mcbond_it 1.681 r_mcbond_other 1.675 r_angle_other_deg 1.125 r_chiral_restr 0.139 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1840 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing