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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 K3(cit), 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 2.94 58.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.21 α = 90 b = 139.35 β = 90 c = 41.71 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 IMAGE PLATE RIGAKU RAXIS IV 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.52
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 1.83 29.605 99.9 0.054 0.054 16.4 5.7 15674 15658 33.3
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 1.83 1.93 99.8 0.755 0.755 1 5.5 2235
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 1.83 29.6 15686 15644 780 99.73 0.198 0.198 0.1966 0.1987 0.2235 0.2247 RANDOM 38.03
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] 0.06 -0.29 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_1_deg 4.434 r_angle_refined_deg 1.606 r_angle_other_deg 1.275 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_1_deg 4.434 r_angle_refined_deg 1.606 r_angle_other_deg 1.275 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 948 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction