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3C-like protease from Southampton virus complexed with FMOPL000324a.
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 0.2 M ammonium citrate, 12% (v/v) PEG3350.
Protein concentration of 5 or 10 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.53 α = 90 b = 88.86 β = 96.65 c = 60.57 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 1.63 60.16 98.5 0.054 0.064 0.035 0.998 12.5 3.3 40339
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 1.63 1.67 99.3 0.716 0.878 0.501 0.534 3.1 3
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 1.63 60.16 38342 1997 98.4 0.1337 0.1301 0.1448 0.2007 0.2076 RANDOM 27.893
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] -0.31 -0.06 0.53 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.793 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 14.55 r_dihedral_angle_1_deg 7.637 r_rigid_bond_restr 3.341 r_angle_refined_deg 1.714 r_angle_other_deg 1.353 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.793 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 14.55 r_dihedral_angle_1_deg 7.637 r_rigid_bond_restr 3.341 r_angle_refined_deg 1.714 r_angle_other_deg 1.353 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2570 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 55
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction REFMAC phasing