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Crystal structure of the fifth bromodomain of human PB1 in complex with compound 28
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 10% MPD, 0.1 M bicine pH 9
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.58 α = 90 b = 62.42 β = 91.75 c = 65.82 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 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) 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 1.55 64.55 90.6 0.053 13.3 4.7 68763 68763
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 1.55 6.93 52.3 0.696 1.5 3.4
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 1.55 64.55 65305 3423 90.44 0.1891 0.18731 0.1969 0.22401 0.2316 RANDOM 29.47
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] -0.47 0.18 -0.14 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.39 r_dihedral_angle_3_deg 15.053 r_dihedral_angle_4_deg 14.137 r_long_range_B_refined 5.444 r_long_range_B_other 5.413 r_dihedral_angle_1_deg 5.079 r_scangle_other 3.88 r_scbond_it 2.454 r_scbond_other 2.454 r_mcangle_it 2.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.39 r_dihedral_angle_3_deg 15.053 r_dihedral_angle_4_deg 14.137 r_long_range_B_refined 5.444 r_long_range_B_other 5.413 r_dihedral_angle_1_deg 5.079 r_scangle_other 3.88 r_scbond_it 2.454 r_scbond_other 2.454 r_mcangle_it 2.308 r_mcangle_other 2.307 r_angle_refined_deg 1.708 r_mcbond_it 1.515 r_mcbond_other 1.514 r_angle_other_deg 1.012 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3688 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing