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Crystal structure of the bromodomain of human BRPF1 in complex with OF-1 chemical probe
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 7.4 277.15 25% PEG3350, 0.1M bis-tris propane pH 7.4, 5% ethyleneglycol, 0.15M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.802 α = 90 b = 60.704 β = 100.43 c = 51.171 γ = 90
Symmetry Space Group I 1 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 2014-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 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 1.65 25.16 99.4 0.042 0.028 18.4 5.9 17300 17300 24.6
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 1.65 1.68 94.2 0.455 3.1 5.3
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 4LC2 1.65 25.16 16439 861 99.37 0.20265 0.19977 0.2083 0.25416 0.25 RANDOM 40.602
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] 2.84 2.06 -2.2 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 21.164 r_dihedral_angle_3_deg 12.438 r_long_range_B_refined 9.424 r_long_range_B_other 9.422 r_scangle_other 7.449 r_dihedral_angle_1_deg 6.091 r_scbond_it 4.809 r_scbond_other 4.805 r_mcangle_other 4.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 21.164 r_dihedral_angle_3_deg 12.438 r_long_range_B_refined 9.424 r_long_range_B_other 9.422 r_scangle_other 7.449 r_dihedral_angle_1_deg 6.091 r_scbond_it 4.809 r_scbond_other 4.805 r_mcangle_other 4.755 r_mcangle_it 4.748 r_mcbond_it 3.285 r_mcbond_other 3.211 r_angle_refined_deg 1.589 r_angle_other_deg 0.819 r_chiral_restr 0.083 r_bond_refined_d 0.014 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 932 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing