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Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F6J PDB ENTRY 2F6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.525 α = 90 b = 38.513 β = 111.2 c = 87.752 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2009-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 1.999 20 98.2 0.061 10.8 7.3 13759
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 1.999 2.05 96.2 0.506 7.1 878
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 2F6J 1.999 20 13758 1044 98.08 0.1863 0.1823 0.2389 0.2342 0.2786 RANDOM 42.786
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] -0.75 0.59 1.95 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.028 r_dihedral_angle_3_deg 15.731 r_dihedral_angle_4_deg 11.741 r_dihedral_angle_1_deg 4.805 r_scangle_it 2.78 r_scbond_it 1.664 r_angle_refined_deg 1.159 r_mcangle_it 0.984 r_mcbond_it 0.511 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.028 r_dihedral_angle_3_deg 15.731 r_dihedral_angle_4_deg 11.741 r_dihedral_angle_1_deg 4.805 r_scangle_it 2.78 r_scbond_it 1.664 r_angle_refined_deg 1.159 r_mcangle_it 0.984 r_mcbond_it 0.511 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1418 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction