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3C-like protease from Southampton virus complexed with XST00000642b.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 294 Protein concentration 4 mg/ml.
0.2 M ammonium citrate and 12% (v/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.153 α = 90 b = 89.507 β = 96.96 c = 61.498 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2016-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.79 51.4 99.8 0.088 0.105 0.057 0.982 6.5 3.3 31951
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 1.79 1.84 99.7 0.551 0.653 0.348 0.804 1.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 6t1q 1.79 51.4 29837 1519 97.81 0.1496 0.1452 0.1584 0.2329 0.2436 RANDOM 27.589
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] -1.06 0.21 -0.34 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.636 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 7.717 r_rigid_bond_restr 2.868 r_angle_refined_deg 1.701 r_angle_other_deg 1.325 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.636 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 7.717 r_rigid_bond_restr 2.868 r_angle_refined_deg 1.701 r_angle_other_deg 1.325 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2570 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 23
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction REFMAC phasing