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MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGN(3,5-diiodotyrosine)PAL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.179 α = 90 b = 90.303 β = 111.58 c = 89.37 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 MARMOSAIC 225 mm CCD 2012-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.3 83.108 99.5 0.077 0.091 0.048 12 3.5 43356 43356
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 99.4 0.529 0.529 0.329 1.5 3.5 6307
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1rjz 2.3 83.108 43337 2178 99.45 0.2135 0.212 0.2428 0.2345 RANDOM 39.719
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] 0.14 -1.41 2.38 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.59 r_dihedral_angle_4_deg 15.194 r_dihedral_angle_3_deg 13.097 r_dihedral_angle_1_deg 6.117 r_mcangle_it 4.222 r_mcbond_it 2.654 r_mcbond_other 2.654 r_angle_refined_deg 1.171 r_angle_other_deg 0.737 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.59 r_dihedral_angle_4_deg 15.194 r_dihedral_angle_3_deg 13.097 r_dihedral_angle_1_deg 6.117 r_mcangle_it 4.222 r_mcbond_it 2.654 r_mcbond_other 2.654 r_angle_refined_deg 1.171 r_angle_other_deg 0.737 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6381 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data scaling PDB_EXTRACT data extraction PHASER phasing XSCALE data scaling