☰ Navigation Tabs
Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GG3 pdb id 3GG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Crystal Properties Matthews coefficient Solvent content 3.38 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.939 α = 90 b = 99.939 β = 90 c = 99.672 γ = 120
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 PSI PILATUS 6M 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.77 19.85 99.9 0.05 16.5 5.1 36188 36.7
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 1.77 1.87 99.9 0.609 2.2 4.3
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 pdb id 3GG3 1.77 19.85 34410 1778 99.9 0.18103 0.17941 0.1858 0.21248 0.2231 RANDOM 45.06
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] -0.06 -0.03 -0.06 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 22.859 r_dihedral_angle_3_deg 12.043 r_long_range_B_refined 8.684 r_long_range_B_other 8.683 r_dihedral_angle_1_deg 5.392 r_scangle_other 5.263 r_scbond_it 3.761 r_scbond_other 3.76 r_mcangle_it 3.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 22.859 r_dihedral_angle_3_deg 12.043 r_long_range_B_refined 8.684 r_long_range_B_other 8.683 r_dihedral_angle_1_deg 5.392 r_scangle_other 5.263 r_scbond_it 3.761 r_scbond_other 3.76 r_mcangle_it 3.342 r_mcangle_other 3.342 r_mcbond_it 2.367 r_mcbond_other 2.366 r_angle_refined_deg 1.566 r_angle_other_deg 1.231 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 1822 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing