7AR0 | pdb_00007ar0

Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB19)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VSG	1VSG, 5lhr(ChainB)
experimental model	PDB	5LHR	1VSG, 5lhr(ChainB)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296.15	0.1 M ADA pH 6.5, 2 M Ammonium Sulfate, 0.1 MgSO4

Crystal Properties
Matthews coefficient	Solvent content
4.33	71.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.738	α = 90
b = 141.738	β = 90
c = 89.582	γ = 90

Symmetry
Space Group	P 41 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2019-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.139	75.726	99.78	0.997	8.7	26.7		50820

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.139	2.216			0.591

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VSG, 5lhr(ChainB)	2.139	75.726	1.34	50754	2448	99.78	0.2071	0.2058	0.2063	0.2338	0.2343	35.8144

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3638
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	39

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
xia2	data scaling
Coot	model building
xia2	data reduction