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Human Class I MHC HLA-A2 in complex with the Peptidomimetic ELA-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GT9 PDB entry 2GT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG3350 24%, MES 0.025M, KCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.208 α = 90 b = 84.222 β = 89.96 c = 83.946 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 CUSTOM-MADE 2007-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98494 APS 19-BM
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 1.8 20 99.6 0.091 13.1 3.7 75477 75175 1 1 17.4
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) 1.8 1.86 97.1 0.523 3.4 7315
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2GT9 1.8 20 75492 75138 3786 99.53 0.1731 0.1731 0.171 0.1913 0.2124 0.2109 RANDOM 21.0633
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] -0.49 -0.2 1.58 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 16.117 r_dihedral_angle_3_deg 15.077 r_dihedral_angle_1_deg 6.979 r_scangle_it 2.732 r_mcangle_it 2.282 r_scbond_it 1.825 r_angle_refined_deg 1.762 r_mcbond_it 1.603 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 16.117 r_dihedral_angle_3_deg 15.077 r_dihedral_angle_1_deg 6.979 r_scangle_it 2.732 r_mcangle_it 2.282 r_scbond_it 1.825 r_angle_refined_deg 1.762 r_mcbond_it 1.603 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.246 r_xyhbond_nbd_refined 0.193 r_nbd_refined 0.16 r_chiral_restr 0.139 r_symmetry_vdw_refined 0.134 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6308 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 54
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling