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Crystal Structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2M Na2SO4
20w/v PEG_3350
10v/v ethylene_glycol
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.79 α = 90 b = 135.664 β = 90.6 c = 56.045 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 IMAGE PLATE RIGAKU RAXIS IV 2011-03-29 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) Rrim I (All) Rpim I (All) 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 1.866 23.819 87.7 0.069 0.069 0.079 0.037 12.1 4.4 44203 44203 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 76.7 0.632 0.632 0.369 1 3.8 5611
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.87 23.8 41808 1782 86.95 0.2026 0.2007 0.208 0.2483 0.2538 RANDOM 27.133
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] 3.57 -0.31 -1.9 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 14.816 r_scangle_it 10.896 r_scbond_it 8.742 r_mcangle_it 5.278 r_dihedral_angle_1_deg 5.129 r_mcbond_it 3.628 r_angle_refined_deg 1.364 r_mcbond_other 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 14.816 r_scangle_it 10.896 r_scbond_it 8.742 r_mcangle_it 5.278 r_dihedral_angle_1_deg 5.129 r_mcbond_it 3.628 r_angle_refined_deg 1.364 r_mcbond_other 1.171 r_angle_other_deg 0.92 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3628 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 60
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction