3BGF | pdb_00003bgf

X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DDB	PDB entries 2DDB, 1KEG
experimental model	PDB	1KEG	PDB entries 2DDB, 1KEG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.688	α = 90
b = 73.365	β = 90
c = 110.782	γ = 90

Symmetry
Space Group	P 21 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	CCD	MAR CCD 165 mm		2006-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.979	NSLS	X12C

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	2.8	50	94.4	0.132	6.3	5.2	37614	35508		-3

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)
	2.8	2.9	69.9		0.751		2.9	2587

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 entries 2DDB, 1KEG	3	30	30760	30321	1495	98.73	0.237	0.234	0.2422	0.286	0.2923	RANDOM	46.995

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]
7.4			-0.5		-6.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.985
r_dihedral_angle_4_deg	14.718
r_dihedral_angle_3_deg	12.486
r_dihedral_angle_1_deg	3.204
r_mcangle_it	1.139
r_angle_refined_deg	1.077
r_mcbond_it	0.647
r_scangle_it	0.548
r_symmetry_hbond_refined	0.426
r_scbond_it	0.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.985
r_dihedral_angle_4_deg	14.718
r_dihedral_angle_3_deg	12.486
r_dihedral_angle_1_deg	3.204
r_mcangle_it	1.139
r_angle_refined_deg	1.077
r_mcbond_it	0.647
r_scangle_it	0.548
r_symmetry_hbond_refined	0.426
r_scbond_it	0.336
r_nbtor_refined	0.328
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.199
r_symmetry_vdw_refined	0.198
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9411
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.