3BOV

Crystal structure of the receptor binding domain of mouse PD-L2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BP5Structure of the model used has to be submitted.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.4 M Magnesium Formate, 0.1 M Tris-HCl pH 8.5, Vapor diffusion, Sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.173α = 90
b = 116.637β = 90
c = 45.108γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.071NSLSX29A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.775098.40.0670.05817.57.31170611706
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.771.8386.30.2790.255.25.51007

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTStructure of the model used has to be submitted.1.7745.13117051170555798.110.1920.1920.190.223RANDOM25.938
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]
1-0.6-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.059
r_dihedral_angle_4_deg22.377
r_dihedral_angle_3_deg12.349
r_dihedral_angle_1_deg5.967
r_scangle_it5.392
r_mcangle_it4.42
r_scbond_it3.953
r_mcbond_it3.11
r_angle_refined_deg1.44
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.059
r_dihedral_angle_4_deg22.377
r_dihedral_angle_3_deg12.349
r_dihedral_angle_1_deg5.967
r_scangle_it5.392
r_mcangle_it4.42
r_scbond_it3.953
r_mcbond_it3.11
r_angle_refined_deg1.44
r_nbtor_refined0.315
r_symmetry_hbond_refined0.267
r_nbd_refined0.213
r_xyhbond_nbd_refined0.192
r_symmetry_vdw_refined0.178
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms856
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing