2A5I

Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in the space group C2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A5A	pdb entry 2A5A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	ammonium acetate, PEG 10000, ethylene glycol, dimethyl sulfoxide, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.703	α = 90
b = 83.677	β = 105.65
c = 52.862	γ = 90

Symmetry
Space Group	C 1 2 1

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	ADSC QUANTUM 210		2004-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115869	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.88	50	96.3				35576

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.95	90

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	pdb entry 2A5A	1.88	40	32587	1710	94.21	0.20034	0.19813	0.24224	RANDOM	43.973

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]
-2.42		1.19	3.69		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.259
r_dihedral_angle_4_deg	17.907
r_dihedral_angle_3_deg	16.83
r_dihedral_angle_1_deg	6.615
r_mcangle_it	2.681
r_scangle_it	2.624
r_angle_refined_deg	2.342
r_scbond_it	2.002
r_mcbond_it	1.919
r_nbtor_refined	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.259
r_dihedral_angle_4_deg	17.907
r_dihedral_angle_3_deg	16.83
r_dihedral_angle_1_deg	6.615
r_mcangle_it	2.681
r_scangle_it	2.624
r_angle_refined_deg	2.342
r_scbond_it	2.002
r_mcbond_it	1.919
r_nbtor_refined	0.34
r_symmetry_hbond_refined	0.329
r_symmetry_vdw_refined	0.308
r_nbd_refined	0.3
r_xyhbond_nbd_refined	0.261
r_chiral_restr	0.192
r_bond_refined_d	0.022
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.