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Crystal structure of the bromodomain of human BRPF1 in complex with a quinolinone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20 % PEG3350, 0.2 M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.315 α = 90 b = 60.315 β = 90 c = 63.389 γ = 120
Symmetry Space Group P 32 2 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 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9686 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.5 27.23 100 0.072 0.024 0.998 17.8 9.5 21838 206811 18.293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.35 0.939 4.9 7.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LC2 1.5 27.23 20751 1061 99.98 0.20755 0.20634 0.23079 0.2604 RANDOM 23.609
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] -0.25 -0.13 -0.25 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.567 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_3_deg 11.157 r_long_range_B_refined 5.531 r_long_range_B_other 5.423 r_dihedral_angle_1_deg 4.691 r_scangle_other 4.218 r_scbond_it 2.738 r_scbond_other 2.735 r_mcangle_other 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.567 r_dihedral_angle_4_deg 17.165 r_dihedral_angle_3_deg 11.157 r_long_range_B_refined 5.531 r_long_range_B_other 5.423 r_dihedral_angle_1_deg 4.691 r_scangle_other 4.218 r_scbond_it 2.738 r_scbond_other 2.735 r_mcangle_other 2.3 r_mcangle_it 2.297 r_angle_refined_deg 1.656 r_mcbond_it 1.654 r_mcbond_other 1.596 r_angle_other_deg 0.856 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 934 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing