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Coxsackievirus B3 3C protease in P121 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Shotgun1 A01
0.1 M Magnesium chloride,
0.1 M TRIS pH 8.2,
25% PEG 4K
Crystal Properties Matthews coefficient Solvent content 1.91 35.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.485 α = 90 b = 45.967 β = 101.559 c = 66.884 γ = 90
Symmetry Space Group P 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 EIGER2 XE 16M 2024-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.59 50.441 81.74 0.993 4.6 6 33816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 0.392
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.592 50.441 28143 1384 68.102 0.214 0.2095 0.2097 0.3008 0.3018 35.562
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] -3.632 1.426 5.924 -2.653
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 26.15 r_lrange_it 26.146 r_scangle_it 22.296 r_scangle_other 22.291 r_mcangle_other 19.462 r_mcangle_it 19.451 r_scbond_it 16.649 r_scbond_other 16.645 r_dihedral_angle_3_deg 16.088 r_dihedral_angle_6_deg 15.493
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 26.15 r_lrange_it 26.146 r_scangle_it 22.296 r_scangle_other 22.291 r_mcangle_other 19.462 r_mcangle_it 19.451 r_scbond_it 16.649 r_scbond_other 16.645 r_dihedral_angle_3_deg 16.088 r_dihedral_angle_6_deg 15.493 r_mcbond_it 14.533 r_mcbond_other 14.498 r_dihedral_angle_2_deg 13.096 r_rigid_bond_restr 11.637 r_dihedral_angle_1_deg 8.591 r_angle_refined_deg 2.585 r_angle_other_deg 1.227 r_symmetry_xyhbond_nbd_refined 0.247 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.192 r_ncsr_local_group_1 0.188 r_nbtor_refined 0.167 r_nbd_other 0.155 r_symmetry_nbd_other 0.154 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.141 r_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2796 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing