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The Crystal Structure of ClpC1-NTD from Biortus.
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, SITTING DROP 293 4.0M Na formate
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.286 α = 90 b = 56.286 β = 90 c = 111.669 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS EIGER X 9M 2020-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18060 CLSI 08ID-1
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 1.85 43.72 100 0.036 29.9 9.5 18178
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 1.85 1.89 0.843 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 43.72 18139 919 99.978 0.176 0.1751 0.1861 0.2008 0.2091 44.855
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] 0.246 0.123 0.246 -0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.802 r_dihedral_angle_6_deg 14.721 r_dihedral_angle_2_deg 12.277 r_lrange_it 10.835 r_lrange_other 10.834 r_scangle_it 9.73 r_scangle_other 9.724 r_scbond_other 7.157 r_scbond_it 7.153 r_mcangle_other 6.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.802 r_dihedral_angle_6_deg 14.721 r_dihedral_angle_2_deg 12.277 r_lrange_it 10.835 r_lrange_other 10.834 r_scangle_it 9.73 r_scangle_other 9.724 r_scbond_other 7.157 r_scbond_it 7.153 r_mcangle_other 6.142 r_mcangle_it 6.126 r_dihedral_angle_1_deg 5.366 r_mcbond_it 4.42 r_mcbond_other 4.417 r_angle_refined_deg 1.422 r_angle_other_deg 0.483 r_xyhbond_nbd_refined 0.268 r_symmetry_xyhbond_nbd_refined 0.268 r_nbd_other 0.238 r_nbd_refined 0.223 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.163 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.073 r_xyhbond_nbd_other 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1126 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing