2GHW | pdb_00002ghw

Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AJF	2AJF CHAIN F, 1DZB CHAIN A
experimental model	PDB	1DZB	2AJF CHAIN F, 1DZB CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	290	12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.453	α = 90
b = 175.902	β = 96.55
c = 67.561	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	CCD	ADSC QUANTUM 4		2005-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.11587	ALS	5.0.3

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	2.29	50	93.8	0.145	8.8	3.1	51915	51915		-4

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)
	2.29	2.38	87		0.571	1.9

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2AJF CHAIN F, 1DZB CHAIN A	2.3	45.55	43380	2308	93.83	0.25085	0.24843	0.26	0.29537	0.27	RANDOM	17.106

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]
-1.64		0.51	-2.58		4.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.323
r_dihedral_angle_3_deg	14.71
r_dihedral_angle_4_deg	13.268
r_dihedral_angle_1_deg	6.662
r_scangle_it	1.308
r_angle_refined_deg	1.217
r_scbond_it	0.877
r_angle_other_deg	0.85
r_mcangle_it	0.612
r_mcbond_it	0.524
r_symmetry_vdw_other	0.191
r_nbd_other	0.19
r_nbtor_refined	0.18
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.171
r_nbd_refined	0.165
r_symmetry_hbond_refined	0.145
r_nbtor_other	0.079
r_chiral_restr	0.073
r_mcbond_other	0.069
r_xyhbond_nbd_other	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6614
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHASER	phasing