5NH0

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherHCoV-NL63 main protease

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 25% PEG 1,000, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
4.371.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.65α = 90
b = 211.29β = 90
c = 118.26γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2014-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.3544.2898.20.0760.0380.99611.54.468423
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)
12.352.4897.20.4580.250.87333.8

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 REPLACEMENTTHROUGHOUTHCoV-NL63 main protease2.3542.8964886352697.980.192050.189850.23196RANDOM43.818
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]
2.09-2.250.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg18.575
r_dihedral_angle_3_deg15.706
r_long_range_B_other9.957
r_long_range_B_refined9.956
r_scangle_other7.838
r_dihedral_angle_1_deg7.033
r_mcangle_it6.283
r_mcangle_other6.282
r_scbond_it5.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg18.575
r_dihedral_angle_3_deg15.706
r_long_range_B_other9.957
r_long_range_B_refined9.956
r_scangle_other7.838
r_dihedral_angle_1_deg7.033
r_mcangle_it6.283
r_mcangle_other6.282
r_scbond_it5.317
r_scbond_other5.317
r_mcbond_it4.319
r_mcbond_other4.316
r_angle_refined_deg1.937
r_angle_other_deg1.24
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms472
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling