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Crystal structure of human PCAF bromodomain in complex with fragment MB364 (fragment 5)
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 3.36 63.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.252 α = 90 b = 99.252 β = 90 c = 100.612 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 2011-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54197
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 2.15 32.68 98.5 0.051 13.2 3.1 19803 33.1
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 2.15 2.27 95.5 0.297 2 2
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 2.15 28.65 18793 1008 98.51 0.1915 0.18934 0.1954 0.23175 0.2339 RANDOM 43.317
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] -0.32 -0.16 -0.32 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 25.729 r_dihedral_angle_3_deg 14.306 r_long_range_B_refined 6.724 r_long_range_B_other 6.723 r_dihedral_angle_1_deg 5.347 r_scangle_other 2.295 r_mcangle_it 1.864 r_mcangle_other 1.864 r_angle_refined_deg 1.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 25.729 r_dihedral_angle_3_deg 14.306 r_long_range_B_refined 6.724 r_long_range_B_other 6.723 r_dihedral_angle_1_deg 5.347 r_scangle_other 2.295 r_mcangle_it 1.864 r_mcangle_other 1.864 r_angle_refined_deg 1.531 r_scbond_it 1.439 r_scbond_other 1.438 r_angle_other_deg 1.343 r_mcbond_it 1.125 r_mcbond_other 1.121 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 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 1800 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction SCALA data scaling PHASER phasing