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Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWE pdb entry 3LWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 35% PEG2000-MME, 8-fold excess of H3K9Me3, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.148 α = 90 b = 74.005 β = 90 c = 72.609 γ = 90
Symmetry Space Group P 21 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 QUANTUM 315 2010-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
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 2.05 50 99.7 0.072 12.6 6.8 24361
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 2.05 2.12 97.6 0.735 5 2340
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 3LWE 2.057 30 24241 1237 99.161 0.222 0.2198 0.2247 0.2732 0.2762 THIN SHELLS (SFTOOLS) 40.273
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] -2.828 0.903 1.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.148 r_dihedral_angle_4_deg 20.282 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 5.878 r_scangle_it 3.238 r_scbond_it 2.019 r_angle_refined_deg 1.369 r_mcangle_it 1.142 r_angle_other_deg 0.803 r_mcbond_it 0.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.148 r_dihedral_angle_4_deg 20.282 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 5.878 r_scangle_it 3.238 r_scbond_it 2.019 r_angle_refined_deg 1.369 r_mcangle_it 1.142 r_angle_other_deg 0.803 r_mcbond_it 0.579 r_mcbond_other 0.138 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2178 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling