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Crystal structure of the bromodomain of human CREBBP in complex with acetylated lysine
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 38.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.687 α = 90 b = 121.687 β = 90 c = 39.955 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 2008-07-13 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 1.6 31.83 100 0.055 0.055 10.7 2.7 19778 19778 25.8
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 1.82 1.92 100 0.434 0.434 1.7 2.6 2895
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 1.82 31.83 19774 19774 1001 100 0.1684 0.1684 0.1658 0.1707 0.218 0.2258 RANDOM 33.8217
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] -1.62 -0.81 -1.62 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 14.33 r_scangle_it 9.774 r_scbond_it 7.49 r_dihedral_angle_1_deg 6.049 r_mcangle_it 4.75 r_mcbond_it 3.515 r_angle_refined_deg 1.509 r_mcbond_other 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 14.33 r_scangle_it 9.774 r_scbond_it 7.49 r_dihedral_angle_1_deg 6.049 r_mcangle_it 4.75 r_mcbond_it 3.515 r_angle_refined_deg 1.509 r_mcbond_other 1.159 r_angle_other_deg 0.977 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1852 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 17
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction