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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Crystal structure of human coronavirus NL63 main protease

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 25% PEG 1,000, 15% glycerol, pH 6.0.

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.862	α = 90
b = 211.327	β = 90
c = 118.317	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225-HS		2013-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	48.24	99.9	0.06	0.067	0.03	0.999	20.4	5		74507

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)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100		0.536	0.262	0.896	3.3	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Crystal structure of human coronavirus NL63 main protease	2.3	48.24	70842	3637	99.84	0.19683	0.19512	0.23116	RANDOM	50.724

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			-3.13		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.143
r_dihedral_angle_4_deg	23.918
r_dihedral_angle_3_deg	16.149
r_long_range_B_refined	11.671
r_long_range_B_other	11.667
r_scangle_other	8.596
r_mcangle_it	8.118
r_mcangle_other	8.117
r_dihedral_angle_1_deg	7.301
r_scbond_it	5.812
r_scbond_other	5.795
r_mcbond_it	5.584
r_mcbond_other	5.584
r_angle_refined_deg	2.1
r_angle_other_deg	1.238
r_chiral_restr	0.118
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	6804
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data processing
SCALA	data scaling
MOLREP	phasing