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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 3.03 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.192 α = 90 b = 88.519 β = 94 c = 120.026 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 MARRESEARCH 2003-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.097 MAX II I711
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 2.95 25 93.6 22159 20741 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 2.95 3.1 89.1
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 1N59 2.95 24.84 22159 19684 1041 93.39 0.24 0.24165 0.23905 0.2426 0.28961 0.2939 RANDOM 23.203
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] 4.19 2.18 -4.87 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.788 r_scangle_it 2.704 r_scbond_it 1.549 r_angle_refined_deg 1.493 r_mcangle_it 1.339 r_angle_other_deg 0.902 r_mcbond_it 0.702 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.255 r_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.788 r_scangle_it 2.704 r_scbond_it 1.549 r_angle_refined_deg 1.493 r_mcangle_it 1.339 r_angle_other_deg 0.902 r_mcbond_it 0.702 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.255 r_nbd_other 0.247 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.19 r_nbtor_other 0.091 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.037 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6276 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing