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Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole 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 9 277.15 0.1 M bis tris propane pH 9, 10% ethylene glycol, 0.15 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.545 α = 90 b = 59.869 β = 100.43 c = 51.236 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 2013-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.55 25.19 98.5 0.037 0.022 19.1 3.7 20656 20656 20.5
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 1.63 97.7 0.402 3.1 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 4LC2 1.55 23.88 19595 1058 98.33 0.18475 0.18319 0.1925 0.2127 0.2178 RANDOM 26.718
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] 1.15 0.73 -0.82 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 20.913 r_dihedral_angle_3_deg 13.227 r_scangle_other 12.7 r_long_range_B_refined 12.122 r_long_range_B_other 12.12 r_scbond_it 9.511 r_scbond_other 9.502 r_mcangle_it 4.94 r_mcangle_other 4.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 20.913 r_dihedral_angle_3_deg 13.227 r_scangle_other 12.7 r_long_range_B_refined 12.122 r_long_range_B_other 12.12 r_scbond_it 9.511 r_scbond_other 9.502 r_mcangle_it 4.94 r_mcangle_other 4.935 r_dihedral_angle_1_deg 4.851 r_mcbond_it 3.983 r_mcbond_other 3.935 r_angle_refined_deg 1.633 r_angle_other_deg 0.794 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 926 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing