2GTB | pdb_00002gtb

Crystal structure of SARS coronavirus main peptidase (with an additional Ala at the N-terminus of each protomer) inhibited by an aza-peptide epoxide in the space group P43212

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	50mM ammonium acetate, 6% PEG 8000, 3% ethylene glycol, 1mM dithiothreitol, 0.1 MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.087	α = 90
b = 70.087	β = 90
c = 103.862	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 210		2004-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.116	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	2	25	99.8				18098

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	2	2.07	99.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	25	17168	923	99.86	0.20031	0.19644	0.1957	0.26971	0.2662	RANDOM	24.336

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]
-1.93			-1.93		3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.409
r_dihedral_angle_4_deg	19.569
r_dihedral_angle_3_deg	18.62
r_dihedral_angle_1_deg	8.103
r_scangle_it	3.66
r_scbond_it	2.744
r_angle_refined_deg	2.064
r_mcangle_it	1.571
r_mcbond_it	1.046
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.143
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2320
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MOLREP	phasing