7ZQW

Structure of the SARS-CoV-1 main protease in complex with AG7404


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UJ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293Lithium Sulfate Monohydrate, HEPES, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9135.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.854α = 90
b = 45.22β = 90
c = 53.55γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97918ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.5353.5591.90.99810.14.27634
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.532.690.431

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 REPLACEMENTTHROUGHOUT1UJ12.5353.55726536983.130.218840.215430.28914RANDOM65.935
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]
-0.6-0.040.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.304
r_dihedral_angle_3_deg20.054
r_dihedral_angle_4_deg18.05
r_long_range_B_refined12.063
r_long_range_B_other12.063
r_scangle_other7.744
r_mcangle_it7.386
r_mcangle_other7.381
r_dihedral_angle_1_deg7.345
r_scbond_it4.728
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2336
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing