3ROL

Murine class I major histocompatibility complex H-2Kb in complex with post-translationally modified LCMV-derived gp34-41 peptide, comprising a nitrotyrosine at position 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S7QPDB ENTRY 1S7Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.72931.8 M NaH2PO4/K2HPO4, 1.5% MPD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
359.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.466α = 90
b = 88.496β = 94.71
c = 119.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.650.31000.1190.11912.94.332268
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)
12.62.751000.393.34.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S7Q2.650.3306303063016541000.2490.2460.295RANDOM31.2
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]
0.03-0.08-0.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.215
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg15.588
r_dihedral_angle_1_deg7.778
r_scangle_it2.6
r_scbond_it1.5
r_angle_refined_deg1.285
r_mcangle_it1.102
r_angle_other_deg0.826
r_mcbond_it0.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.215
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg15.588
r_dihedral_angle_1_deg7.778
r_scangle_it2.6
r_scbond_it1.5
r_angle_refined_deg1.285
r_mcangle_it1.102
r_angle_other_deg0.826
r_mcbond_it0.573
r_mcbond_other0.101
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6176
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms24

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling