2AJF | pdb_00002ajf

Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R42	PDB ENTRY 1R42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		100 mM Tris pH 8.2, 24% PEG6000, 150 mM NaCl, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, pH 7.5, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.299	α = 90
b = 119.429	β = 91.97
c = 113.237	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				2005-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	47.4	93.1	0.085	20.5	6.9		41841

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	93.1		0.682	1.83

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1R42	2.9	47.4	41841	2165	92.4	0.221	0.218	0.2151	0.275	0.2713	RANDOM	90.77

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]
0.45		7.05	0.04		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.497
r_dihedral_angle_3_deg	20.62
r_dihedral_angle_4_deg	17.319
r_dihedral_angle_1_deg	5.69
r_scangle_it	1.433
r_angle_refined_deg	1.253
r_mcangle_it	1.234
r_scbond_it	0.855
r_mcbond_it	0.678
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.24
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.22
r_xyhbond_nbd_refined	0.17
r_metal_ion_refined	0.167
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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_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	12546
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	166

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing