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3C-like protease from Southampton virus complexed with FMOPL000014a.
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 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.8 α = 90 b = 89.26 β = 96.67 c = 61.49 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 1.42 61.07 96.4 0.034 0.042 0.023 0.999 15 2.9 60967
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 1.42 1.46 86.8 0.672 0.908 0.605 0.502 2.1
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 1.42 61.07 57938 3026 96.19 0.1343 0.1312 0.131 0.1947 0.1947 RANDOM 26.087
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] 0.01 -0.24 -0.31 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.906 r_dihedral_angle_4_deg 16.315 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 7.495 r_rigid_bond_restr 4.718 r_angle_refined_deg 2.037 r_angle_other_deg 1.438 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.906 r_dihedral_angle_4_deg 16.315 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 7.495 r_rigid_bond_restr 4.718 r_angle_refined_deg 2.037 r_angle_other_deg 1.438 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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 395 Heterogen Atoms 15
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction REFMAC phasing