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Crystal Structure of the bromodomain of human BAZ2B in complex with compound-6 E11322
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0L pdb entry 3G0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 28% low MW PEG Smears, 0.1M MES pH 6.5, 15%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 4.16 70.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.477 α = 90 b = 96.377 β = 90 c = 57.705 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 2011-11-22 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 1.85 19.52 99.8 0.078 11.4 5 19728 19706 29.5
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 1.85 1.95 100 0.658 2.1 5 2816
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 pdb entry 3G0L 1.85 19.52 2 19706 18697 1007 99.65 0.17896 0.17725 0.187 0.21227 0.2229 RANDOM 38.842
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] 2.47 -0.9 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.187 r_dihedral_angle_4_deg 23.244 r_dihedral_angle_3_deg 12.812 r_long_range_B_refined 10.094 r_long_range_B_other 10.093 r_scangle_other 7.423 r_dihedral_angle_1_deg 6.033 r_scbond_it 5.921 r_scbond_other 5.919 r_mcangle_other 4.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.187 r_dihedral_angle_4_deg 23.244 r_dihedral_angle_3_deg 12.812 r_long_range_B_refined 10.094 r_long_range_B_other 10.093 r_scangle_other 7.423 r_dihedral_angle_1_deg 6.033 r_scbond_it 5.921 r_scbond_other 5.919 r_mcangle_other 4.885 r_mcangle_it 4.85 r_mcbond_it 4.013 r_mcbond_other 3.99 r_angle_refined_deg 1.567 r_angle_other_deg 0.937 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 937 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 37
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling