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Structure of the S. pombe Clr4 catalytic domain bound to SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MVH PDB entry 1MVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M magnesium formate dihydrate and 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.76 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.919 α = 90 b = 71.04 β = 125.06 c = 96.674 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 100 CCD ADSC QUANTUM 315r 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7701 79.14 77.15 0.125 0.084 0.995 6.5 2.94 14482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7701 2.9839 0.712 0.48 0.328
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 1MVH 2.7701 59.349 1.34 14482 704 77.02 0.2248 0.2228 0.2215 0.2644 0.2658
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.87 f_angle_d 0.585 f_chiral_restr 0.041 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing