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Crystal structures of the murine class I major histocompatibility complex H-2Db 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 1N5A PDB entry 1N5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Ammonium sulfate, Tris , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.13 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.389 α = 90 b = 123.343 β = 103.17 c = 99.392 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 2002-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 2.2 72.7 99 109867 108769 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 2.2 2.42 99
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 1N5A 2.2 72.7 103314 5426 99 0.21569 0.21327 0.2133 0.26222 0.2597 RANDOM 25.562
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] 0.51 -0.01 0.49 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.33 r_scangle_it 2.327 r_scbond_it 1.368 r_angle_refined_deg 1.203 r_mcangle_it 1.148 r_angle_other_deg 0.784 r_mcbond_it 0.606 r_symmetry_vdw_other 0.276 r_nbd_other 0.234 r_nbd_refined 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.33 r_scangle_it 2.327 r_scbond_it 1.368 r_angle_refined_deg 1.203 r_mcangle_it 1.148 r_angle_other_deg 0.784 r_mcbond_it 0.606 r_symmetry_vdw_other 0.276 r_nbd_other 0.234 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.151 r_nbtor_other 0.085 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12577 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing