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Crystal structure of BRD9 Bromodomain bound to a butyryllysine 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 0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.117 α = 90 b = 69.825 β = 90 c = 104.554 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 2013-02-24 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 2 50 95.2 0.091 8 4.3 8638
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 2 2.07 83.5 0.632 4 747
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 2.1 33.12 7156 346 95.8 0.2557 0.253 0.2375 0.3115 0.293 RANDOM 35.98
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] 3.42 -5.07 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_3_deg 18.897 r_dihedral_angle_4_deg 11.999 r_dihedral_angle_1_deg 4.971 r_scbond_it 3.525 r_mcangle_it 3.36 r_mcbond_it 2.639 r_angle_refined_deg 1.967 r_chiral_restr 0.132 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_3_deg 18.897 r_dihedral_angle_4_deg 11.999 r_dihedral_angle_1_deg 4.971 r_scbond_it 3.525 r_mcangle_it 3.36 r_mcbond_it 2.639 r_angle_refined_deg 1.967 r_chiral_restr 0.132 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 815 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction