5NH0 | pdb_00005nh0

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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		HCoV-NL63 main protease

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
4.3	71.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.65	α = 90
b = 211.29	β = 90
c = 118.26	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 MX225HE		2014-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.35	44.28	98.2	0.076	0.038	0.996	11.5	4.4		68423

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	2.35	2.48	97.2		0.458	0.25	0.873	3	3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	HCoV-NL63 main protease	2.35	42.89	64886	3526	97.98	0.19205	0.18985	0.2	0.23196	0.23	RANDOM	43.818

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			-2.25		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.36
r_dihedral_angle_4_deg	18.575
r_dihedral_angle_3_deg	15.706
r_long_range_B_other	9.957
r_long_range_B_refined	9.956
r_scangle_other	7.838
r_dihedral_angle_1_deg	7.033
r_mcangle_it	6.283
r_mcangle_other	6.282
r_scbond_it	5.317
r_scbond_other	5.317
r_mcbond_it	4.319
r_mcbond_other	4.316
r_angle_refined_deg	1.937
r_angle_other_deg	1.24
r_chiral_restr	0.128
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
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	472
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling