2BX3 | pdb_00002bx3

Crystal Structure of SARS Coronavirus Main Proteinase (P43212)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UJ1	PDB ENTRY 1UJ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.9		15% PEG6000, 0.1M MES PH 5.9, 3% MPD

Crystal Properties
Matthews coefficient	Solvent content
1.8	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.675	α = 90
b = 69.675	β = 90
c = 100.197	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	100	IMAGE PLATE	MARRESEARCH		2004-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	40.82	100	0.15	20.6	15.6		17333		2	20.32

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	99.8		0.56	4.9	13.9

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UJ1	2	56.8	16395	884	99.9	0.18	0.175	0.19	0.257	RANDOM	20.36

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]
-1.77			-1.77		3.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.603
r_dihedral_angle_4_deg	21.846
r_dihedral_angle_3_deg	16.821
r_dihedral_angle_1_deg	9.207
r_mcangle_it	2.183
r_scangle_it	1.925
r_angle_refined_deg	1.718
r_mcbond_it	1.709
r_scbond_it	1.347
r_angle_other_deg	0.818
r_symmetry_hbond_refined	0.307
r_symmetry_vdw_refined	0.3
r_xyhbond_nbd_refined	0.29
r_symmetry_vdw_other	0.267
r_nbd_refined	0.229
r_nbd_other	0.209
r_nbtor_refined	0.197
r_chiral_restr	0.117
r_nbtor_other	0.099
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing