1R6F | pdb_00001r6f

The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	294	PEG 5000 MME, sodium acetate, Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.881	α = 76.2
b = 45.086	β = 78.42
c = 46.915	γ = 77.17

Symmetry
Space Group	P 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		2002-01-15	M	MAD
2	1		CCD	ADSC QUANTUM 4		2002-01-15

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.9795, 0.9790, 0.9719	NSLS	X9A
2	SYNCHROTRON	NSLS BEAMLINE X9B	0.9715	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.17	18.5	95.9	0.077	0.077	12.5	2.2	14116	14116	-3	-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)
	2.17	2.25	86.2		0.37	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	2.17	18.5	14116	14116	1383	96.22	0.224	0.224	0.217	0.27	0.284	0.26	Random	27.251

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]
-2.29	2.2	-1.8	-0.4	-2.91	3.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.237
r_scangle_it	3.068
r_scbond_it	2.124
r_angle_refined_deg	1.877
r_mcangle_it	1.088
r_mcbond_it	0.629
r_nbd_refined	0.307
r_xyhbond_nbd_refined	0.263
r_symmetry_vdw_refined	0.247
r_symmetry_hbond_refined	0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.237
r_scangle_it	3.068
r_scbond_it	2.124
r_angle_refined_deg	1.877
r_mcangle_it	1.088
r_mcbond_it	0.629
r_nbd_refined	0.307
r_xyhbond_nbd_refined	0.263
r_symmetry_vdw_refined	0.247
r_symmetry_hbond_refined	0.22
r_chiral_restr	0.131
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2139
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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

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.