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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 3.09 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.22 α = 90 b = 135.871 β = 90 c = 45.168 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 2003-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.97 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 1.99 141.42 98.9 38269 37848 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) 1.99 2.1 94
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 37.53 38269 35920 1894 98.79 0.18281 0.18142 0.2128 0.20933 0.2352 RANDOM 18.251
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] 0.04 0.18 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.621 r_scangle_it 4.228 r_scbond_it 2.544 r_mcangle_it 1.605 r_angle_refined_deg 1.488 r_angle_other_deg 0.889 r_mcbond_it 0.821 r_nbd_other 0.255 r_symmetry_vdw_other 0.227 r_nbd_refined 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.621 r_scangle_it 4.228 r_scbond_it 2.544 r_mcangle_it 1.605 r_angle_refined_deg 1.488 r_angle_other_deg 0.889 r_mcbond_it 0.821 r_nbd_other 0.255 r_symmetry_vdw_other 0.227 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.183 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.11 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3130 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing