1FZJ

MHC CLASS I NATURAL MUTANT H-2KBM1 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.4290K/Na phosphate, MPD, pH 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.91α = 90
b = 88.35β = 90
c = 45.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
11.91599.20.05620.33.343138431382.516.2
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)
11.91.9398.90.4052.53.32102

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 DIFFRACTIONCNS, done by rigid body refinement of starting model.THROUGHOUTpdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine.1.91541155206294.60.2040.2040.222RANDOM29.2
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]
-4.177.52-3.35
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it2.59
c_mcangle_it1.67
c_scbond_it1.66
c_angle_deg1.6
c_improper_angle_d1.14
c_mcbond_it1.05
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3123
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms86

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing