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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 3.18 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.469 α = 90 b = 91.184 β = 125 c = 92.147 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARRESEARCH 2003-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 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 32 94.4 55257 52163 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) 2.2 2.257 94.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1N5A 2.2 32.44 2 55257 49523 2639 94.41 0.22761 0.2256 0.26678 0.2942 RANDOM 19.852
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] 2.26 1.62 1.72 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.953 r_scangle_it 2.661 r_scbond_it 1.671 r_angle_refined_deg 1.401 r_mcangle_it 1.145 r_angle_other_deg 0.924 r_mcbond_it 0.634 r_symmetry_hbond_refined 0.358 r_symmetry_vdw_other 0.271 r_nbd_other 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.953 r_scangle_it 2.661 r_scbond_it 1.671 r_angle_refined_deg 1.401 r_mcangle_it 1.145 r_angle_other_deg 0.924 r_mcbond_it 0.634 r_symmetry_hbond_refined 0.358 r_symmetry_vdw_other 0.271 r_nbd_other 0.262 r_xyhbond_nbd_refined 0.235 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.125 r_nbtor_other 0.09 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6207 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing