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ClpC N-terminal domain with bound phospho-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292 The optimized crystallization solution contained 13.5% w/w polyethylene glycol
4000, 500 mM ammonium sulphate, and 100 mM sodium acetate at pH 5. Hexagonal crystals of space group P 6(5) formed overnight at 19C and were cryo-protected in 40% polyethylene glycol 400, 20 mM Tris pH 8, and 6 mM pArgAA prior to being flash-frozen.
Crystal Properties Matthews coefficient Solvent content 1.8 31.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.6 α = 90 b = 84.6 β = 90 c = 29.85 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2015-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.9763 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.602 42.3 98.19 0.06169 0.06347 29.81 18.6 16041
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 2Y1Q 1.602 42.3 1.41 16041 1585 98.19 0.1469 0.1447 0.1474 0.166 0.1672
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 21.287 f_angle_d 1.08 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1105 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing