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Crystal structure of the bromodomain of human CREBBP in complex with N-Methyl-2-pyrrolidone (NMP)
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
20% PEG3350
5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.01 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.549 α = 90 b = 121.549 β = 90 c = 40.23 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 2009-10-29 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 1.86 19.76 99.9 0.067 0.067 11.8 3.7 18632 18613
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 1.86 1.96 100 0.629 0.629 1.2 3.6
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 (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 1.86 19.76 18609 17665 942 99.99 0.16952 0.167 0.1678 0.21819 0.2113 RANDOM 28.168
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] -0.87 -0.43 -0.87 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.004 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.682 r_scangle_it 8.686 r_scbond_it 7.334 r_dihedral_angle_1_deg 6.117 r_mcangle_it 4.901 r_mcbond_it 3.456 r_angle_refined_deg 1.5 r_mcbond_other 1.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.004 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.682 r_scangle_it 8.686 r_scbond_it 7.334 r_dihedral_angle_1_deg 6.117 r_mcangle_it 4.901 r_mcbond_it 3.456 r_angle_refined_deg 1.5 r_mcbond_other 1.126 r_angle_other_deg 0.952 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1859 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction