4DZB

Mucosal-associated invariant T cell receptor, Valpha7.2Jalpha33-Vbeta2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NX5pdb entry 2NX5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529825% PEG 1500, 0.1M MIB buffer (sodium malonate, imidazole, boric acid), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.962α = 90
b = 64.515β = 90
c = 155.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2005-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95453Australian SynchrotronMX2

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
11.75097.10.09313.77.6459574462417.5
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)
11.71.7992.60.7732.57.46281

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 2NX51.7504499043627232596.970.192640.190670.23063RANDOM18.68
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]
0.440.01-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.387
r_dihedral_angle_3_deg12.652
r_dihedral_angle_4_deg12.061
r_dihedral_angle_1_deg6.347
r_scangle_it4.184
r_scbond_it2.595
r_mcangle_it1.75
r_angle_refined_deg1.5
r_mcbond_it0.981
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.387
r_dihedral_angle_3_deg12.652
r_dihedral_angle_4_deg12.061
r_dihedral_angle_1_deg6.347
r_scangle_it4.184
r_scbond_it2.595
r_mcangle_it1.75
r_angle_refined_deg1.5
r_mcbond_it0.981
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3424
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling