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Crystal Structure of MHC class I HLA-A2 molecule complexed with Human Prostaglandin Transporter decapeptide
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 15% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 3mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.887 α = 90 b = 81.041 β = 114.66 c = 57.505 γ = 90
Symmetry Space Group P 1 21 1
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 2009-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9834 ESRF ID23-2
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 1.6 50 93.7 0.032 21.82 3.43 55551 -3 31.354
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 1.6 1.7 71.3 0.408 2.1
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 1.6 14.89 55478 5572 93.85 0.194 0.192 0.1975 0.224 0.2033 RANDOM 33.406
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.326 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.644 r_scangle_it 5.178 r_scbond_it 3.317 r_mcangle_it 2.469 r_mcbond_it 1.448 r_angle_refined_deg 1.196 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.326 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.644 r_scangle_it 5.178 r_scbond_it 3.317 r_mcangle_it 2.469 r_mcbond_it 1.448 r_angle_refined_deg 1.196 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3152 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing