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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 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.897 α = 90 b = 123.318 β = 102.82 c = 100.201 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 2003-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.007 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 2.41 19.8 98.2 84548 83027 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) 2.41 2.54 89.3
Refinement Statistics Diffraction ID Structure Solution 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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1N5A 2.41 19.8 2 84548 83027 19840 0.2058 0.203 0.254 0.2974 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.709 r_scbond_it 1.421 r_angle_refined_deg 1.25 r_mcangle_it 1.202 r_angle_other_deg 0.803 r_mcbond_it 0.631 r_symmetry_vdw_other 0.257 r_nbd_other 0.232 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.709 r_scbond_it 1.421 r_angle_refined_deg 1.25 r_mcangle_it 1.202 r_angle_other_deg 0.803 r_mcbond_it 0.631 r_symmetry_vdw_other 0.257 r_nbd_other 0.232 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.184 r_nbtor_other 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12616 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling