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Crystal structure of BRD9 bromodomain in complex with an indolizine 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 6.5 277.15 0.2 M NaNO3, 0.1 M BTProp pH 6.5, 20% PEG 3350, 10% EtGly
Crystal Properties Matthews coefficient Solvent content 2.26 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.381 α = 90 b = 37.96 β = 106.17 c = 60.551 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 2013-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.8 29.66 99.4 0.065 0.041 19.5 6.6 23830
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 1.8 1.84 96.2 0.657 2.9 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HME 1.8 29.66 22590 1224 99.3 0.19511 0.19318 0.23089 0.2241 RANDOM 27.681
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] 0.65 0.97 -0.91 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.506 r_dihedral_angle_4_deg 13.262 r_dihedral_angle_3_deg 12.929 r_long_range_B_refined 5.521 r_long_range_B_other 5.52 r_dihedral_angle_1_deg 4.685 r_scangle_other 3.54 r_scbond_it 2.252 r_scbond_other 2.251 r_mcangle_it 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.506 r_dihedral_angle_4_deg 13.262 r_dihedral_angle_3_deg 12.929 r_long_range_B_refined 5.521 r_long_range_B_other 5.52 r_dihedral_angle_1_deg 4.685 r_scangle_other 3.54 r_scbond_it 2.252 r_scbond_other 2.251 r_mcangle_it 2.117 r_mcangle_other 2.116 r_angle_refined_deg 1.574 r_mcbond_other 1.388 r_mcbond_it 1.387 r_angle_other_deg 0.995 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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 136 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing