2QIQ

Structure-based Design and Synthesis and Biological Evaluation of Peptidomimetic SARS-3CLpro Inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG 20000, Na Cacodylate, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
3.4764.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.325α = 90
b = 82.225β = 104.67
c = 53.684γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.92032745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9291.50.310.196

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ALV1.92031114163191.270.2350.2330.275RANDOM46.646
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]
-1.230.91.290.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.567
r_dihedral_angle_4_deg17.911
r_dihedral_angle_3_deg15.644
r_dihedral_angle_1_deg6.978
r_scangle_it2.643
r_scbond_it1.915
r_mcangle_it1.782
r_angle_refined_deg1.502
r_mcbond_it1.056
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.567
r_dihedral_angle_4_deg17.911
r_dihedral_angle_3_deg15.644
r_dihedral_angle_1_deg6.978
r_scangle_it2.643
r_scbond_it1.915
r_mcangle_it1.782
r_angle_refined_deg1.502
r_mcbond_it1.056
r_nbtor_refined0.307
r_nbd_refined0.214
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.145
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2332
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing