3TH0 | pdb_00003th0

P22 Tailspike complexed with S.Paratyphi O antigen octasaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VFM	ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ
experimental model	PDB	2VFN	ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ
experimental model	PDB	2VFQ	ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	277.15	1.5 Ammonium sulfate, 0.1M sodium phosphate over reservoir 1.0 Ammonium sulfate, 0.1M sodium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
2	MICRODIALYSIS	7.5	293.15	addition of 2mM S.Paratyphi o antigen octasaccharide in 0.1M Tris, 1M sodium phosphate, pH 7.5, MICRODIALYSIS, temperature 293.15K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.943	α = 90
b = 119.943	β = 90
c = 119.943	γ = 90

Symmetry
Space Group	P 21 3

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	RAYONIX MX-225	mirrors, double crystal monochromator, MD2 microdiffractometer, MK3-minikappa	2010-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.75	33.27	99.9	0.133	16.1	5.7		58030			11.55

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	99.9		3.2	5.2	4247

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	ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ	1.75	33.27	55128	2902	99.91	0.13682	0.13578	0.13	0.15588	0.15	RANDOM	10.308

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.937
r_dihedral_angle_3_deg	11.173
r_dihedral_angle_4_deg	9.842
r_dihedral_angle_1_deg	6.671
r_scangle_it	2.814
r_scbond_it	1.719
r_angle_refined_deg	1.372
r_mcangle_it	1.028
r_angle_other_deg	0.831
r_mcbond_it	0.566
r_mcbond_other	0.153
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4182
Nucleic Acid Atoms
Solvent Atoms	660
Heterogen Atoms	101

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling