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Crystal structure of the fifth bromodomain of human PB1 in complex with compound 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 0.1 M magnesium formate, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.98 α = 90 b = 59.21 β = 90 c = 138.9 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2015-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.47 59.21 95.2 0.052 0.02 21.4 7.8 56934 56934
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 6.57 68.3 0.565 2.1 2.8
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 4Q0O 1.47 54.53 54004 2857 94.93 0.18785 0.18681 0.1961 0.2085 0.2213 RANDOM 24.183
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] 0.07 0.59 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.908 r_dihedral_angle_4_deg 15.505 r_dihedral_angle_3_deg 12.296 r_long_range_B_refined 6.017 r_long_range_B_other 5.813 r_dihedral_angle_1_deg 4.668 r_scangle_other 3.667 r_scbond_it 2.274 r_scbond_other 2.273 r_mcangle_it 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.908 r_dihedral_angle_4_deg 15.505 r_dihedral_angle_3_deg 12.296 r_long_range_B_refined 6.017 r_long_range_B_other 5.813 r_dihedral_angle_1_deg 4.668 r_scangle_other 3.667 r_scbond_it 2.274 r_scbond_other 2.273 r_mcangle_it 1.93 r_mcangle_other 1.929 r_angle_refined_deg 1.649 r_mcbond_it 1.242 r_mcbond_other 1.241 r_angle_other_deg 0.979 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing