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Crystal structure of BRD9 Bromodomain bound to DMSO
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 7.5 277 0.1 M HEPES, pH 7.5, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.145 α = 90 b = 68.546 β = 90 c = 105.176 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX300-HS mirrors 2012-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.47 50 96.5 0.053 10.6 5.8 21295
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 1.47 1.52 80.8 0.452 4.9 1746
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 1.47 32.59 20147 1087 96.26 0.2178 0.2169 0.2099 0.2343 0.2274 RANDOM 28.83
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] 0.33 3.48 -3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.178 r_dihedral_angle_4_deg 26.017 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 4.664 r_scbond_it 4.153 r_mcangle_it 3.327 r_angle_refined_deg 2.764 r_mcbond_it 2.45 r_chiral_restr 0.2 r_bond_refined_d 0.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.178 r_dihedral_angle_4_deg 26.017 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 4.664 r_scbond_it 4.153 r_mcangle_it 3.327 r_angle_refined_deg 2.764 r_mcbond_it 2.45 r_chiral_restr 0.2 r_bond_refined_d 0.032 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 825 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 4
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing