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Crystal structure of the bromodomain of human BRPF1 in complex with NI-48 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 0.1 m bis-tris propane pH 8.5, 0.2 M sodium formate, 20% PEG 3350, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.086 α = 90 b = 60.145 β = 99.83 c = 51.948 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 2014-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.65 25.59 99 0.045 0.034 0.998 16.5 5.1 17186 87628 23.407
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 1.65 1.67 97.6 0.5 0.897 2.9 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LC2 1.65 25.59 16311 874 98.87 0.21204 0.2099 0.2165 0.25044 0.2588 RANDOM 35.233
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] 1.98 1.97 -1.36 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 22.682 r_dihedral_angle_3_deg 11.82 r_dihedral_angle_1_deg 5.717 r_angle_refined_deg 1.586 r_angle_other_deg 0.854 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 22.682 r_dihedral_angle_3_deg 11.82 r_dihedral_angle_1_deg 5.717 r_angle_refined_deg 1.586 r_angle_other_deg 0.854 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 928 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing