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Structure of ClpC1-NTD bound to a CymA analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 100 mM MES/imidazole pH 6.5, 6% (w/v) PEG 20K, 2% (v/v) PEG MME 550, 120 mM 1,6-hexanediol, 120 mM (RS)-1,2-propanediol, 120 mM 2-propanol, 120 mM 1,4-butanediol
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.35 α = 86.18 b = 33.68 β = 94.22 c = 35.81 γ = 103.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.68 25 93.8 0.062 0.998 22.6 5.8 15176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 86.5 0.112 0.992 12.5 5.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3WDB 1.68 24.77 1.99 15165 757 93.81 0.1714 0.1696 0.1689 0.2033 0.2005 Random selection
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 26.756 f_angle_d 0.789 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1291 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MAR345dtb data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building