2GTZ

Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A28L substitution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TVBPDB entry 1TVB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG 3350 24%, MES 0.025M, NH4Cl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3247.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.4α = 90
b = 84.31β = 90.13
c = 84.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.979APS23-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
11.720970.113.13.59021087504116.7
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)
11.71.7685.60.4792.12.67671

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1TVB1.72019018583098438296.950.174120.174120.171840.2173RANDOM21.719
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]
-0.690.171.6-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.731
r_dihedral_angle_4_deg20.887
r_dihedral_angle_3_deg14.818
r_dihedral_angle_1_deg6.135
r_scangle_it4.624
r_scbond_it2.882
r_angle_refined_deg1.71
r_mcangle_it1.701
r_mcbond_it0.939
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.731
r_dihedral_angle_4_deg20.887
r_dihedral_angle_3_deg14.818
r_dihedral_angle_1_deg6.135
r_scangle_it4.624
r_scbond_it2.882
r_angle_refined_deg1.71
r_mcangle_it1.701
r_mcbond_it0.939
r_nbtor_refined0.309
r_symmetry_hbond_refined0.199
r_metal_ion_refined0.192
r_xyhbond_nbd_refined0.189
r_nbd_refined0.162
r_chiral_restr0.154
r_symmetry_vdw_refined0.124
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6288
Nucleic Acid Atoms
Solvent Atoms812
Heterogen Atoms38

Software

Software
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling