1P9S | pdb_00001p9s

Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LVO	PDB ENTRY 1LVO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	283	PEG 10000, 1,6-hexanediol, DTT, HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.356	α = 90
b = 76.24	β = 103.7
c = 73.477	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MARRESEARCH		2000-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.9801	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.54	70.71		0.142	9.1	12.3	17709	17709

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LVO	2.54	70.71	17709	17709	965	98.22	0.20068	0.19639	0.27887	RANDOM	28.781

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]
0.18		0.55	-0.91		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.547
r_mcangle_it	2.295
r_scangle_it	2.214
r_angle_refined_deg	1.836
r_scbond_it	1.399
r_mcbond_it	1.343
r_angle_other_deg	1.104
r_symmetry_vdw_other	0.367
r_symmetry_hbond_refined	0.361
r_nbd_other	0.27
r_nbd_refined	0.252
r_xyhbond_nbd_refined	0.211
r_symmetry_vdw_refined	0.163
r_chiral_restr	0.103
r_nbtor_other	0.102
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4589
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing