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Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E6I PDB ENTRY 1E6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 3.23 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.3 α = 90 b = 101.3 β = 90 c = 79.35 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC CCD 2007-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.1 40 91.2 0.11 7 7.7 22542 60.7
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 2.1 2.2 93.9 0.61 2.9 8
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 PDB ENTRY 1E6I 2.1 40 22542 1143 91.2 0.234 0.234 0.2231 0.255 0.2025 RANDOM 72.1
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] -0.052 -0.052 0.104
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.4 c_angle_deg 1.20706 c_improper_angle_d 0.96 c_bond_d 0.007812 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.4 c_angle_deg 1.20706 c_improper_angle_d 0.96 c_bond_d 0.007812 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2036 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling MOLREP phasing