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Thermococcus gammatolerans DNA Ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 291 HEPES 0.08M pH7, 2-propanol 8.5%, PEG 4000 5%, [7.7mg/ml protein]
Crystal Properties Matthews coefficient Solvent content 3.34 63.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.65 α = 90 b = 93.7 β = 90 c = 97.05 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 PIXEL DECTRIS PILATUS3 X 6M 2022-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 2.17 40 99.9 0.107 0.113 0.03773 0.998 11.4 8.97 45418 58
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 2.17 2.27 100 2.646 2.806 0.9915 0.752 9.111698
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.17 39.07 1.33 41467 1919 91.4 0.2174 0.2155 0.2155 0.258 0.2576 72.05
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 7.339 f_angle_d 1.077 f_chiral_restr 0.056 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4445 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing