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chromo shadow domain of CBX1 in complex with a histone peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FMM pdb entry 2FMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.5 M sodium citrate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.657 α = 90 b = 76.887 β = 90 c = 78.1 γ = 90
Symmetry Space Group F 2 2 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 315r 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9791827 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.8 43.07 99.9 0.075 0.081 0.03 0.999 16.9 7.2 9891
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.4 1.478 1.596 0.596 0.788 1.3 6.9 564
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2FMM 1.9 43.07 7611 839 99.88 0.2156 0.2126 0.224 0.2431 0.2617 34.927
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] 0.43 3.28 -3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_3_deg 10.735 r_dihedral_angle_1_deg 5.847 r_dihedral_angle_4_deg 2.403 r_mcangle_it 2.065 r_angle_refined_deg 1.48 r_mcbond_it 1.275 r_mcbond_other 1.275 r_angle_other_deg 0.931 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_3_deg 10.735 r_dihedral_angle_1_deg 5.847 r_dihedral_angle_4_deg 2.403 r_mcangle_it 2.065 r_angle_refined_deg 1.48 r_mcbond_it 1.275 r_mcbond_other 1.275 r_angle_other_deg 0.931 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 487 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing