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Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MB4 PDB ENTRY 3MB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.20M Na(malonate), 0.1M BTProp pH 6.5, 20.0% PEG 3350
10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.021 α = 90 b = 136.722 β = 91.4 c = 114.413 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 2M 2012-05-09 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 1.78 29.687 97 0.052 0.052 11.8 2.6 123195 119499 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.88 96.6 0.484 0.484 1.5 2.5 17332
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3MB4 1.78 26.69 213233 119437 1938 96.92 0.1762 0.1762 0.1756 0.1858 0.2142 0.2174 RANDOM 29.313
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] 1.18 0.3 -0.45 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_4_deg 15.048 r_mcangle_it 5.79 r_mcbond_it 5.071 r_dihedral_angle_1_deg 5.065 r_mcbond_other 5.055 r_angle_refined_deg 1.579 r_angle_other_deg 0.86 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_4_deg 15.048 r_mcangle_it 5.79 r_mcbond_it 5.071 r_dihedral_angle_1_deg 5.065 r_mcbond_other 5.055 r_angle_refined_deg 1.579 r_angle_other_deg 0.86 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7380 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 196
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction