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Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HME PDB entry 3HME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES, pH 6.5, 15% w/v PEG550 MME
Crystal Properties Matthews coefficient Solvent content 2.04 39.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.84 α = 89.88 b = 34.73 β = 89.81 c = 129.08 γ = 69.45
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 MARMOSAIC 300 mm CCD 2012-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.68 50 96.6 0.089 13 3.7 38297 36333
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 1.68 1.74 99.9 0.617 3.1 2412
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 PDB entry 3HME 1.79 32.27 34482 1851 94.87 0.2271 0.2252 0.1951 0.2612 0.2209 RANDOM 29.101
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] -1.52 -0.84 0.2 8.16 -2.82 -6.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.941 r_dihedral_angle_4_deg 24.631 r_dihedral_angle_3_deg 20.322 r_dihedral_angle_1_deg 7.772 r_mcangle_it 3.973 r_scbond_it 3.56 r_mcbond_it 3.122 r_angle_refined_deg 2.846 r_chiral_restr 0.21 r_bond_refined_d 0.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.941 r_dihedral_angle_4_deg 24.631 r_dihedral_angle_3_deg 20.322 r_dihedral_angle_1_deg 7.772 r_mcangle_it 3.973 r_scbond_it 3.56 r_mcbond_it 3.122 r_angle_refined_deg 2.846 r_chiral_restr 0.21 r_bond_refined_d 0.028 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction