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Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 with dGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 0.2M Potassium Thiocyanate
20% PEG 3350
10mM MnCl2
2mM dGTP
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.953 α = 90 b = 62.675 β = 90 c = 82.484 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 100 PIXEL DECTRIS EIGER2 XE 16M 2018-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.28 62.68 99.2 0.08 0.088 0.036 0.999 9.6 5.9 53746 14.19
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 1.28 1.3 90.6 1.642 1.914 0.956 0.284 1 3.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NQD 1.28 49.9 1.34 53569 2636 98.88 0.1643 0.1629 0.1901 0.1875 20.76
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 6.7307 f_angle_d 1.0072 f_chiral_restr 0.0881 f_plane_restr 0.0067 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement DIALS data reduction xia2 data scaling PHASER phasing Coot model building