☰ Navigation Tabs
Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.828 α = 90 b = 128.591 β = 104.7 c = 45.847 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 4 2005-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.3 50 97.7 0.048 3.7 22955 22434 -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) 2.3 2.38 97.9 0.166 3.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DVV 2.3 20 21151 1144 98.03 0.20447 0.20096 0.26757 RANDOM 43.691
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] 1.78 1.26 -0.85 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.94 r_scangle_it 3.728 r_scbond_it 2.753 r_mcangle_it 2.424 r_angle_refined_deg 1.871 r_mcbond_it 1.489 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.94 r_scangle_it 3.728 r_scbond_it 2.753 r_mcangle_it 2.424 r_angle_refined_deg 1.871 r_mcbond_it 1.489 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.12 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3766 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing