6FV1

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide (S)-N-((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)-2-cinnamamido-4-methylpentanamide (cinnamoyl-leucine-GlnLactam-CO-CO-NH-benzyl)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal structure of human coronavirus NL63 main protease

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 25% PEG 1,000, 15% glycerol, pH 6.0.
Crystal Properties
Matthews coefficientSolvent content
4.270.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.862α = 90
b = 211.327β = 90
c = 118.317γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2013-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.348.2499.90.060.0670.030.99920.4574507
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421000.5360.2620.8963.35

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 REPLACEMENTTHROUGHOUTCrystal structure of human coronavirus NL63 main protease2.348.2470842363799.840.196830.195120.23116RANDOM50.724
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]
2.44-3.130.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg23.918
r_dihedral_angle_3_deg16.149
r_long_range_B_refined11.671
r_long_range_B_other11.667
r_scangle_other8.596
r_mcangle_it8.118
r_mcangle_other8.117
r_dihedral_angle_1_deg7.301
r_scbond_it5.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg23.918
r_dihedral_angle_3_deg16.149
r_long_range_B_refined11.671
r_long_range_B_other11.667
r_scangle_other8.596
r_mcangle_it8.118
r_mcangle_other8.117
r_dihedral_angle_1_deg7.301
r_scbond_it5.812
r_scbond_other5.795
r_mcbond_it5.584
r_mcbond_other5.584
r_angle_refined_deg2.1
r_angle_other_deg1.238
r_chiral_restr0.118
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6804
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
autoXDSdata processing
SCALAdata scaling
MOLREPphasing