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Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LVO PDB ENTRY 1LVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 283 PEG 10000, 1,6-hexanediol, DTT, HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.356 α = 90 b = 76.24 β = 103.7 c = 73.477 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MARRESEARCH 2000-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.9801 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.54 70.71 0.142 9.1 12.3 17709 17709
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LVO 2.54 70.71 17709 17709 965 98.22 0.20068 0.19639 0.27887 RANDOM 28.781
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] 0.18 0.55 -0.91 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.547 r_mcangle_it 2.295 r_scangle_it 2.214 r_angle_refined_deg 1.836 r_scbond_it 1.399 r_mcbond_it 1.343 r_angle_other_deg 1.104 r_symmetry_vdw_other 0.367 r_symmetry_hbond_refined 0.361 r_nbd_other 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.547 r_mcangle_it 2.295 r_scangle_it 2.214 r_angle_refined_deg 1.836 r_scbond_it 1.399 r_mcbond_it 1.343 r_angle_other_deg 1.104 r_symmetry_vdw_other 0.367 r_symmetry_hbond_refined 0.361 r_nbd_other 0.27 r_nbd_refined 0.252 r_xyhbond_nbd_refined 0.211 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.103 r_nbtor_other 0.102 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4589 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing