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Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide
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 5.5 277.15 25% PEG3350, 0.2 M MgCl2, 0.1 M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.266 α = 90 b = 74.354 β = 90 c = 49.509 γ = 90
Symmetry Space Group P 21 21 2
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 2014-10-13 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 1.3 29.73 98.6 0.086 0.027 17.5 11.1 67343 67343 13.37
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 1.3 1.37 90.3 0.425 4.5 8.3
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 1.3 29.73 63980 3307 98.55 0.19077 0.18997 0.1996 0.20636 0.213 RANDOM 18.865
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 -0.34 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.336 r_dihedral_angle_4_deg 12.259 r_dihedral_angle_3_deg 10.483 r_dihedral_angle_1_deg 5.076 r_long_range_B_refined 4.799 r_long_range_B_other 4.597 r_scangle_other 2.716 r_scbond_it 1.731 r_scbond_other 1.731 r_mcangle_it 1.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.336 r_dihedral_angle_4_deg 12.259 r_dihedral_angle_3_deg 10.483 r_dihedral_angle_1_deg 5.076 r_long_range_B_refined 4.799 r_long_range_B_other 4.597 r_scangle_other 2.716 r_scbond_it 1.731 r_scbond_other 1.731 r_mcangle_it 1.642 r_mcangle_other 1.642 r_angle_refined_deg 1.333 r_mcbond_it 1.046 r_mcbond_other 1.043 r_angle_other_deg 0.776 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 1938 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing