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Crystal structure of the bromodomain of human CREBBP in complex with dimethyl sulfoxide (DMSO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2M KSCN
25% PEG3350
5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.85 α = 90 b = 121.85 β = 90 c = 40.55 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 IMAGE PLATE RIGAKU RAXIS IV 2010-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 28.435 99.9 0.095 0.095 4.8 2.3 20837 20816 23.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 99.9 0.456 0.456 1.1 2.2 3057
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3DWY 1.8 28.435 20832 20807 1050 99.88 0.1823 0.1823 0.1795 0.1798 0.2357 0.231 RANDOM 26.326
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] -0.31 -0.16 -0.31 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.29 r_dihedral_angle_4_deg 21.518 r_dihedral_angle_3_deg 13.9 r_scangle_it 8.67 r_scbond_it 6.577 r_dihedral_angle_1_deg 5.513 r_mcangle_it 4.45 r_mcbond_it 3.272 r_angle_refined_deg 1.45 r_mcbond_other 1.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.29 r_dihedral_angle_4_deg 21.518 r_dihedral_angle_3_deg 13.9 r_scangle_it 8.67 r_scbond_it 6.577 r_dihedral_angle_1_deg 5.513 r_mcangle_it 4.45 r_mcbond_it 3.272 r_angle_refined_deg 1.45 r_mcbond_other 1.104 r_angle_other_deg 0.97 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1846 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 12
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction