3D0G | pdb_00003d0g

Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.008	α = 90
b = 119.762	β = 96.22
c = 108.801	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							SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97924	APS	19-BM

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	2.8	50					50660

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	47.14	44939	2262	93.81	0.217	0.214	0.2451	0.279	RANDOM	74.503

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]
0.44		3.72	1.93		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.657
r_dihedral_angle_3_deg	20.043
r_dihedral_angle_4_deg	17.461
r_dihedral_angle_1_deg	5.765
r_sphericity_free	5.227
r_mcangle_it	1.853
r_scangle_it	1.8
r_angle_refined_deg	1.27
r_scbond_it	1.126
r_rigid_bond_restr	1.055
r_mcbond_it	1.031
r_sphericity_bonded	0.842
r_nbtor_refined	0.315
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.09
r_metal_ion_refined	0.059
r_symmetry_hbond_refined	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12522
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing