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Crystal Structure of the bromodomain of human BAZ2B in complex with E11919 BAZ2-ICR analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 36% Low Molecular Weight PEG Smears (LMW PEG smears), 0.1M MES pH 6.5 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution)
Crystal Properties Matthews coefficient Solvent content 4.16 70.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.64 α = 90 b = 96.01 β = 90 c = 57.83 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV 2011-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.75 33.35 98.4 0.053 15.2 5.1 22857 30.6
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 1.75 1.84 96.7 0.479 2.5 5.1
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 3G0L 1.75 29.8 21664 1168 98.05 0.18179 0.17986 0.1859 0.21904 0.2244 RANDOM 37.197
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] 1.61 -0.75 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.145 r_dihedral_angle_4_deg 17.985 r_dihedral_angle_3_deg 13.955 r_dihedral_angle_1_deg 5.542 r_angle_refined_deg 1.605 r_angle_other_deg 1.081 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.145 r_dihedral_angle_4_deg 17.985 r_dihedral_angle_3_deg 13.955 r_dihedral_angle_1_deg 5.542 r_angle_refined_deg 1.605 r_angle_other_deg 1.081 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 941 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing