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Crystal structure of human PCAF bromodomain in complex with compound SL1122 (compound 13)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.076 α = 90 b = 100.076 β = 90 c = 99.821 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 2012-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54167
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 2.35 32.72 99.8 0.076 14.4 5.6 15504 47.5
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 2.35 2.48 98.8 0.622 2 4.1
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 3GG3 2.35 32.72 14724 776 99.77 0.20365 0.20094 0.2039 0.25828 0.2584 RANDOM 55.817
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_4_deg 24.764 r_dihedral_angle_3_deg 15.239 r_long_range_B_refined 6.258 r_long_range_B_other 6.256 r_dihedral_angle_1_deg 5.704 r_scangle_other 2.877 r_mcangle_it 2.179 r_mcangle_other 2.178 r_scbond_it 1.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_4_deg 24.764 r_dihedral_angle_3_deg 15.239 r_long_range_B_refined 6.258 r_long_range_B_other 6.256 r_dihedral_angle_1_deg 5.704 r_scangle_other 2.877 r_mcangle_it 2.179 r_mcangle_other 2.178 r_scbond_it 1.722 r_scbond_other 1.721 r_angle_refined_deg 1.337 r_mcbond_it 1.286 r_mcbond_other 1.285 r_angle_other_deg 1.183 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 1805 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction SCALA data scaling PHASER phasing