3SBW

Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7755.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.778α = 90
b = 62.843β = 90
c = 160.863γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-08-21MSINGLE 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)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
12.285099.90.0937.66.12681626816
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.381000.7296.12628

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NPU2.2831.4226756133999.110.2210.21840.2704RANDOM43.3543
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]
-0.33-1.722.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.774
r_dihedral_angle_4_deg21.329
r_dihedral_angle_3_deg16.418
r_dihedral_angle_1_deg6.423
r_scangle_it2.969
r_scbond_it1.84
r_angle_refined_deg1.421
r_mcangle_it1.295
r_mcbond_it0.69
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.774
r_dihedral_angle_4_deg21.329
r_dihedral_angle_3_deg16.418
r_dihedral_angle_1_deg6.423
r_scangle_it2.969
r_scbond_it1.84
r_angle_refined_deg1.421
r_mcangle_it1.295
r_mcbond_it0.69
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3429
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms

Software

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