3MRR

Crystal Structure of MHC class I HLA-A2 molecule complexed with Human Prostaglandin Transporter decapeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRPPDB ENTRY 3MRP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529315% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 3mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.887α = 90
b = 81.041β = 114.66
c = 57.505γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.9834ESRFID23-2

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
11.65093.70.03221.823.4355551-331.354
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)
11.61.771.30.4082.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3MRP1.614.8955478557293.850.1940.1920.224RANDOM33.406
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.326
r_dihedral_angle_4_deg16.62
r_dihedral_angle_3_deg13.379
r_dihedral_angle_1_deg5.644
r_scangle_it5.178
r_scbond_it3.317
r_mcangle_it2.469
r_mcbond_it1.448
r_angle_refined_deg1.196
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.326
r_dihedral_angle_4_deg16.62
r_dihedral_angle_3_deg13.379
r_dihedral_angle_1_deg5.644
r_scangle_it5.178
r_scbond_it3.317
r_mcangle_it2.469
r_mcbond_it1.448
r_angle_refined_deg1.196
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3152
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing