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Crystal structure of BRD9 Bromodomain bound to an acetylated 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 Bis-Tris, pH 6.5, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.746 α = 88.79 b = 34.602 β = 90 c = 129.361 γ = 68.92
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 2013-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.000 APS 23-ID-D
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 1.5 50 95.1 0.05 11.1 2.3 60687
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 1.5 1.55 94 0.304 2.3 6045
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 1.5 32.28 57639 3019 94.5 0.2077 0.206 0.2225 0.2422 0.2515 RANDOM 26.997
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] 2.92 0.83 -0.43 -2.79 -0.45 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 16.345 r_dihedral_angle_1_deg 6.571 r_scbond_it 3.159 r_mcangle_it 3.102 r_angle_refined_deg 2.752 r_mcbond_it 2.516 r_chiral_restr 0.193 r_bond_refined_d 0.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 16.345 r_dihedral_angle_1_deg 6.571 r_scbond_it 3.159 r_mcangle_it 3.102 r_angle_refined_deg 2.752 r_mcbond_it 2.516 r_chiral_restr 0.193 r_bond_refined_d 0.028 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3352 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction