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Crystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N59 PDB entry 1N59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 sodium/potassium phosphate, Methyl pentane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.08 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.262 α = 90 b = 135.555 β = 90 c = 45.13 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2003-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.069 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.99 50 92.9 39141 36362 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.1 80.7
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 (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 1N59 1.99 19.88 39141 33520 1750 92.86 0.19206 0.19001 0.2027 0.23191 0.2441 RANDOM 21.868
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] 0.03 0.11 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.796 r_scangle_it 4.304 r_scbond_it 2.641 r_angle_refined_deg 1.694 r_mcangle_it 1.601 r_angle_other_deg 0.936 r_mcbond_it 0.859 r_symmetry_vdw_other 0.268 r_nbd_other 0.261 r_nbd_refined 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.796 r_scangle_it 4.304 r_scbond_it 2.641 r_angle_refined_deg 1.694 r_mcangle_it 1.601 r_angle_other_deg 0.936 r_mcbond_it 0.859 r_symmetry_vdw_other 0.268 r_nbd_other 0.261 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.123 r_chiral_restr 0.112 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3131 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing