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3C-like protease from Southampton virus complexed with FMOPL000283a.
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 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.02 α = 90 b = 89.72 β = 96.67 c = 61.53 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 2016-10-05 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 1.67 24.53 97 0.046 0.055 0.03 0.999 15.2 3.2 38160
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 1.67 1.71 95.7 0.796 0.995 0.587 0.469 1.3 2.8
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 1.67 24.53 36305 1849 96.84 0.1323 0.1283 0.1403 0.2099 0.2156 RANDOM 32.547
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] -0.84 0.31 0.87 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.039 r_dihedral_angle_4_deg 16.501 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 8.013 r_rigid_bond_restr 4.004 r_angle_refined_deg 1.811 r_angle_other_deg 1.337 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.039 r_dihedral_angle_4_deg 16.501 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 8.013 r_rigid_bond_restr 4.004 r_angle_refined_deg 1.811 r_angle_other_deg 1.337 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2577 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction REFMAC phasing