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Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02857790
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 calcium acetate hydrate, and 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.283 α = 90 b = 34.321 β = 106.82 c = 40.005 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 MARMOSAIC 225 mm CCD 2015-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9786 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.07 50 99 0.069 0.083 0.045 11.6 3.5 53632
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 1.07 1.11 97.3 0.207 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3DWY 1.07 45.13 50979 2653 98.94 0.1176 0.1165 0.1371 0.1585 RANDOM 13.397
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] -0.09 -0.09 0.26 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.246 r_sphericity_free 34.5 r_sphericity_bonded 14.702 r_dihedral_angle_3_deg 11.977 r_dihedral_angle_4_deg 10.181 r_rigid_bond_restr 6.971 r_dihedral_angle_1_deg 6.335 r_mcangle_it 4.983 r_mcbond_it 3.939 r_mcbond_other 3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.246 r_sphericity_free 34.5 r_sphericity_bonded 14.702 r_dihedral_angle_3_deg 11.977 r_dihedral_angle_4_deg 10.181 r_rigid_bond_restr 6.971 r_dihedral_angle_1_deg 6.335 r_mcangle_it 4.983 r_mcbond_it 3.939 r_mcbond_other 3.935 r_angle_refined_deg 1.38 r_angle_other_deg 0.726 r_chiral_restr 0.076 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 967 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing