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Crystal structure of human PCAF bromodomain in complex with fragment MB360 (fragment 4)
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 3.4 63.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.721 α = 90 b = 99.721 β = 90 c = 100.742 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 CCD Bruker Platinum 135 2011-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54399
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 2.12 32.78 99.3 0.065 13.9 5.3 21067 33.4
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 2.12 2.23 97.8 0.368 2 3.1
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 2.12 28.79 19977 1086 99.33 0.19997 0.19801 0.2038 0.23693 0.2436 RANDOM 41.77
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] -0.1 -0.05 -0.1 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.171 r_dihedral_angle_4_deg 20.042 r_dihedral_angle_3_deg 12.917 r_long_range_B_refined 7.388 r_long_range_B_other 7.386 r_dihedral_angle_1_deg 5.26 r_scangle_other 2.258 r_mcangle_it 1.639 r_mcangle_other 1.638 r_angle_refined_deg 1.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.171 r_dihedral_angle_4_deg 20.042 r_dihedral_angle_3_deg 12.917 r_long_range_B_refined 7.388 r_long_range_B_other 7.386 r_dihedral_angle_1_deg 5.26 r_scangle_other 2.258 r_mcangle_it 1.639 r_mcangle_other 1.638 r_angle_refined_deg 1.451 r_scbond_it 1.426 r_scbond_other 1.425 r_angle_other_deg 1.275 r_mcbond_it 0.995 r_mcbond_other 0.995 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.007 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 1821 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction SCALA data scaling PHASER phasing