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Crystal structure of human BAZ2A bromodomain in complex with a diacetylated histone 4 peptide (H4K16acK20ac)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LZ2 pdb entry 4LZ2, BAZ2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1M sodium phosphate monobasic, 0.1M potassium phosphate monobasic, 2 M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.869 α = 90 b = 64.869 β = 90 c = 71.637 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9763 Diamond I04-1
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 1.65 29.01 0.067 0.036 15.6 8.5 35633 35633 18.75
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 pdb entry 4LZ2, BAZ2A 1.65 64.87 35633 33458 1661 98.22 0.18631 0.18534 0.1943 0.20495 0.2134 RANDOM 23.668
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] 0.24 0.24 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.843 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_3_deg 11.079 r_long_range_B_refined 5.377 r_long_range_B_other 5.248 r_dihedral_angle_1_deg 5.136 r_scangle_other 3.629 r_scbond_it 2.284 r_scbond_other 2.282 r_mcangle_other 2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.843 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_3_deg 11.079 r_long_range_B_refined 5.377 r_long_range_B_other 5.248 r_dihedral_angle_1_deg 5.136 r_scangle_other 3.629 r_scbond_it 2.284 r_scbond_other 2.282 r_mcangle_other 2.134 r_mcangle_it 2.132 r_angle_refined_deg 1.386 r_mcbond_it 1.359 r_mcbond_other 1.353 r_angle_other_deg 0.795 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1905 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling