1KPU

High resolution crystal structure of the MHC class I complex H-2Kb/VSV8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VAAPDB entry 2vaa, chains A and B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0659.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.086α = 90
b = 88.121β = 90
c = 45.24γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2001-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.033APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.54292.50.1139.86.381282-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5571.50.4312.93.76180

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 REPLACEMENTTHROUGHOUTPDB entry 2vaa, chains A and B1.541.8974678397796.850.185520.184320.20814RANDOM17.187
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]
-0.410.55-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.108
r_scangle_it4.609
r_dihedral_angle_1_deg4.602
r_angle_other_deg3.173
r_scbond_it2.755
r_mcangle_it1.902
r_angle_refined_deg1.643
r_mcbond_it1.008
r_nbtor_other0.434
r_symmetry_vdw_other0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.108
r_scangle_it4.609
r_dihedral_angle_1_deg4.602
r_angle_other_deg3.173
r_scbond_it2.755
r_mcangle_it1.902
r_angle_refined_deg1.643
r_mcbond_it1.008
r_nbtor_other0.434
r_symmetry_vdw_other0.299
r_symmetry_vdw_refined0.234
r_nbd_refined0.216
r_xyhbond_nbd_other0.204
r_nbd_other0.201
r_chiral_restr0.169
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.12
r_bond_refined_d0.014
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3121
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing