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MHC Class I in complex with Sendai virus nucleoprotein peptide FAPGNYPAL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P9L
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 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.721 α = 90 b = 136.533 β = 90 c = 45.203 γ = 90
Symmetry Space Group P 21 21 2
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 2012-07-02 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 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 2.4 40 98.3 0.127 0.127 8.3 3.8 21454 21454 20.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.53 98.9 0.488 0.488 2.6 3.8
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 3P9L 2.4 40 21436 1101 97.5 0.2124 0.2104 0.2153 0.2499 0.2569 RANDOM 26.523
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] -1.16 0.56 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.404 r_dihedral_angle_4_deg 14.439 r_dihedral_angle_3_deg 12.453 r_dihedral_angle_1_deg 5.747 r_mcangle_it 1.303 r_angle_refined_deg 1.01 r_mcbond_it 0.747 r_mcbond_other 0.747 r_angle_other_deg 0.682 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.404 r_dihedral_angle_4_deg 14.439 r_dihedral_angle_3_deg 12.453 r_dihedral_angle_1_deg 5.747 r_mcangle_it 1.303 r_angle_refined_deg 1.01 r_mcbond_it 0.747 r_mcbond_other 0.747 r_angle_other_deg 0.682 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3136 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 60
Software Software Software Name Purpose SCALA data scaling XDS data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement