8TBQ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6OIL 
experimental modelPDB 6MVL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M BIS-TRIS propane, 0.2 M NaBr, 22%PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.659α = 90
b = 39.512β = 117.121
c = 177.979γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9998SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.593158.40984.60.9968.94.2726185
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5932.83752.70.6954.58

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.593158.40926185129163.90.2390.23660.240.2910.2951.929
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]
0.294-0.481-0.970.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.999
r_dihedral_angle_3_deg12.86
r_dihedral_angle_1_deg7.227
r_lrange_it5.205
r_lrange_other5.202
r_dihedral_angle_2_deg3.639
r_mcangle_it3.35
r_mcangle_other3.35
r_scangle_it2.401
r_scangle_other2.401
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8440
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing