2YNA

Crystal structure of the main protease of coronavirus HKU4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TNTPDB ENTRY 3TNT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9293SITTING-DROP VAPOR DIFFUSION AT 20C, 6% W/V POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2-PROPANOL, 0.1 M IMIDAZOLE PH 6.9.
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.624α = 90
b = 79.624β = 90
c = 178.37γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2012-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.5178.3799.60.0532.411105128-317.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5295.40.584.38.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3TNT1.568.96105041524799.540.15760.15660.1754RANDOM22.68
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]
-0.5609-0.56091.1218
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.11
t_omega_torsion4.68
t_angle_deg1.11
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.11
t_omega_torsion4.68
t_angle_deg1.11
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4618
Nucleic Acid Atoms
Solvent Atoms827
Heterogen Atoms31

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
XDSdata scaling
SCALAdata scaling
MOLREPphasing