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Crystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide
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 3.41 63.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.859 α = 90 b = 99.859 β = 90 c = 100.762 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 DECTRIS PILATUS3 S 6M 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91997 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 2.05 65.62 100 0.054 13.9 4.8 23526 49.9
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 2.05 2.16 100 0.616 2.6 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.05 43.54 22306 1212 99.95 0.18235 0.18045 0.1865 0.21795 0.2221 RANDOM 62.896
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 22.177 r_dihedral_angle_3_deg 15.344 r_long_range_B_refined 9.815 r_long_range_B_other 9.814 r_scangle_other 7.155 r_dihedral_angle_1_deg 5.812 r_mcangle_it 5.316 r_mcangle_other 5.315 r_scbond_it 4.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 22.177 r_dihedral_angle_3_deg 15.344 r_long_range_B_refined 9.815 r_long_range_B_other 9.814 r_scangle_other 7.155 r_dihedral_angle_1_deg 5.812 r_mcangle_it 5.316 r_mcangle_other 5.315 r_scbond_it 4.866 r_scbond_other 4.864 r_mcbond_it 3.778 r_mcbond_other 3.776 r_angle_refined_deg 1.712 r_angle_other_deg 1.202 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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 1792 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing