8TBQ | pdb_00008tbq

The crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6OIL
experimental model	PDB	6MVL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1 M BIS-TRIS propane, 0.2 M NaBr, 22%PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.659	α = 90
b = 39.512	β = 117.121
c = 177.979	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS EIGER2 X 16M		2022-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9998	SLS	X10SA

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	2.593	158.409	84.6	0.996	8.9	4.27		26185

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	2.593	2.837	52.7		0.695		4.58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.593	158.409	26185	1291	63.9	0.239	0.2366	0.24	0.291	0.29	51.929

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]
0.294		-0.481	-0.97		0.766

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.999
r_dihedral_angle_3_deg	12.86
r_dihedral_angle_1_deg	7.227
r_lrange_it	5.205
r_lrange_other	5.202
r_dihedral_angle_2_deg	3.639
r_mcangle_it	3.35
r_mcangle_other	3.35
r_scangle_it	2.401
r_scangle_other	2.401
r_mcbond_it	1.9
r_mcbond_other	1.9
r_scbond_it	1.332
r_scbond_other	1.332
r_angle_refined_deg	0.941
r_angle_other_deg	0.577
r_nbtor_refined	0.158
r_symmetry_nbd_other	0.155
r_nbd_refined	0.145
r_xyhbond_nbd_refined	0.107
r_nbd_other	0.107
r_symmetry_xyhbond_nbd_refined	0.088
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.074
r_ncsr_local_group_3	0.061
r_ncsr_local_group_1	0.045
r_chiral_restr	0.044
r_ncsr_local_group_2	0.041
r_bond_other_d	0.026
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8440
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing