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Crystal Structure of MHC class I HLA-A2 molecule complexed with Melan-A MART1 decapeptide variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRP PDB ENTRY 3MRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 17% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 2.61mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.874 α = 90 b = 80.044 β = 90 c = 110.571 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2007-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9500 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 50 100 0.129 12.17 7.12 28175 -3 28.072
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.449 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3MRP 2.2 14.84 28009 2801 100 0.193 0.192 0.1947 0.235 0.1978 RANDOM 31.322
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.627 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_1_deg 6.131 r_scangle_it 2.687 r_scbond_it 1.715 r_angle_refined_deg 1.219 r_mcangle_it 1.118 r_mcbond_it 0.703 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.627 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_1_deg 6.131 r_scangle_it 2.687 r_scbond_it 1.715 r_angle_refined_deg 1.219 r_mcangle_it 1.118 r_mcbond_it 0.703 r_nbtor_refined 0.296 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.147 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3145 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing