7NMG

Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BCK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29125% PEG 1500, 0.1M PCTP Buffer, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.32α = 90
b = 72.13β = 90
c = 230.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.4852.9399.80.0950.1080.050.99711.64.433057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.482.5899.91.311.4860.690.5134.4

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 REPLACEMENTTHROUGHOUT2BCK2.4852.9331375161699.70.20130.19770.271RANDOM51.78
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]
0.83-0.15-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.545
r_dihedral_angle_4_deg19.025
r_dihedral_angle_3_deg18.286
r_dihedral_angle_1_deg9.396
r_angle_refined_deg1.452
r_angle_other_deg1.183
r_chiral_restr0.064
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.545
r_dihedral_angle_4_deg19.025
r_dihedral_angle_3_deg18.286
r_dihedral_angle_1_deg9.396
r_angle_refined_deg1.452
r_angle_other_deg1.183
r_chiral_restr0.064
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6598
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
XDSdata reduction