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Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02773986
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 277.15 0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.832 α = 90 b = 50.885 β = 90 c = 80.534 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 2012-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 1.35 50 99.8 0.08 10.2 5.7 30903
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 1.35 1.4 100 0.631 5.8
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 PDB entry 3DWY 1.35 31.58 29268 1551 99.41 0.1467 0.1444 0.1457 0.1877 0.1901 RANDOM 20.686
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] -0.49 2.37 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.639 r_sphericity_free 27.356 r_dihedral_angle_4_deg 13.534 r_sphericity_bonded 12.354 r_dihedral_angle_3_deg 12.35 r_rigid_bond_restr 6.094 r_dihedral_angle_1_deg 5.769 r_mcangle_it 2.746 r_mcbond_it 2.33 r_mcbond_other 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.639 r_sphericity_free 27.356 r_dihedral_angle_4_deg 13.534 r_sphericity_bonded 12.354 r_dihedral_angle_3_deg 12.35 r_rigid_bond_restr 6.094 r_dihedral_angle_1_deg 5.769 r_mcangle_it 2.746 r_mcbond_it 2.33 r_mcbond_other 2.24 r_angle_refined_deg 1.463 r_angle_other_deg 0.758 r_chiral_restr 0.093 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 962 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 25
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing