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Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JVJ PDB ENTRY 3JVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.004 α = 90 b = 47.232 β = 90 c = 77.977 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2009-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978946 SLS X10SA
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 1.65 19.6 99.5 0.08 20.8 15640 15640 -3 -3
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) 1.65 1.7 98.8 0.502 4.1
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 3JVJ 1.65 19.6 14813 14813 815 99.51 0.18046 0.17799 0.1835 0.22578 0.2307 RANDOM 24.305
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] 4.04 -1.92 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_1_deg 5.708 r_scangle_it 5.19 r_scbond_it 3.507 r_mcangle_it 2.531 r_angle_refined_deg 2.114 r_mcbond_it 1.618 r_chiral_restr 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_1_deg 5.708 r_scangle_it 5.19 r_scbond_it 3.507 r_mcangle_it 2.531 r_angle_refined_deg 2.114 r_mcbond_it 1.618 r_chiral_restr 0.43 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1057 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing