6VRM

T cell receptor-p53-HLA-A2 complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D2L5D2L, 3SJV, 2AK4
experimental modelPDB 3SJV5D2L, 3SJV, 2AK4
experimental modelPDB 2AK45D2L, 3SJV, 2AK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729520% (w/v) polyacrylic acid 5100, 0.1 M HEPES, 20 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.1460.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.405α = 90
b = 120.608β = 108.38
c = 119.693γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-ID-D

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
12.6137.998.40.04412.22.636118
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)
12.612.70.343

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 REPLACEMENTTHROUGHOUT5D2L, 3SJV, 2AK42.6119.7934121188898.160.19490.19050.2753RANDOM75.679
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]
0.160.09-0.08-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.487
r_dihedral_angle_4_deg20.568
r_dihedral_angle_3_deg18.776
r_dihedral_angle_1_deg8.441
r_rigid_bond_restr6.967
r_angle_refined_deg1.752
r_chiral_restr0.126
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6282
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing