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Crystal structure of the bromodomain of human CREBBP in complex with an oxazepin ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWY PDB entry 3DWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.10M MgCl2, 0.1M MES pH 6.0, 20.0% PEG 6K, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.71 α = 90 b = 35.14 β = 93 c = 40.4 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2012-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0121 Diamond I04
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 1.66 30.79 99 0.063 0.063 10.7 3.4 15041 14891 21.4
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 1.66 1.75 97.9 0.478 0.478 1.6 3.1 2113
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 PDB entry 3DWY 1.66 30.79 15062 14889 749 98.85 0.1809 0.1809 0.1784 0.1841 0.2305 0.245 RANDOM 29.1493
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] -1.27 -0.52 2.6 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.307 r_dihedral_angle_4_deg 21.922 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 5.93 r_angle_refined_deg 1.698 r_angle_other_deg 0.956 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.307 r_dihedral_angle_4_deg 21.922 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 5.93 r_angle_refined_deg 1.698 r_angle_other_deg 0.956 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 965 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 34
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction