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Murine class I major histocompatibility complex H-2Kb in complex with immunodominant LCMV-derived gp34-41 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7Q pdb entry 1S7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 2.1 M NaH2PO4/K2HPO4, 1.5% MPD, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.448 α = 90 b = 92.588 β = 90 c = 128.827 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 4 2000-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 57.3 99.9 0.083 0.083 11.6 4.7 72101 72101
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 100 0.67 2.6 4.6 10411
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 1S7Q 2 57.26 68459 68459 3635 99.9 0.2272 0.22511 0.2295 0.2671 0.2709 RANDOM 33.688
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] -0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.984 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 5.815 r_scangle_it 2.649 r_scbond_it 1.558 r_mcangle_it 1.225 r_angle_refined_deg 1.131 r_angle_other_deg 0.8 r_mcbond_it 0.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.984 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 5.815 r_scangle_it 2.649 r_scbond_it 1.558 r_mcangle_it 1.225 r_angle_refined_deg 1.131 r_angle_other_deg 0.8 r_mcbond_it 0.648 r_mcbond_other 0.101 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6213 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 38
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling