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CL3E peptide bound to the I-Ab murine MHC class II receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.2 M magnesium chloride hexahydrate, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.7 54.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.057 α = 90 b = 76.032 β = 90 c = 133.037 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS 6M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979181 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 46.85 99.2 0.087 0.112 0.07 0.997 7.5 4.3 30076 40.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.936 1.199 0.739 0.783 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 46.85 30056 1495 98.732 0.219 0.2165 0.2235 0.263 0.2678 45.744
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] 6.844 -6.063 -0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.107 r_dihedral_angle_6_deg 12.761 r_lrange_it 8.475 r_lrange_other 8.475 r_dihedral_angle_1_deg 7.97 r_scangle_it 7.083 r_scangle_other 7.082 r_dihedral_angle_2_deg 6.054 r_mcangle_it 5.897 r_mcangle_other 5.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.107 r_dihedral_angle_6_deg 12.761 r_lrange_it 8.475 r_lrange_other 8.475 r_dihedral_angle_1_deg 7.97 r_scangle_it 7.083 r_scangle_other 7.082 r_dihedral_angle_2_deg 6.054 r_mcangle_it 5.897 r_mcangle_other 5.896 r_scbond_it 5.195 r_scbond_other 5.193 r_mcbond_it 4.307 r_mcbond_other 4.304 r_angle_refined_deg 1.688 r_angle_other_deg 0.588 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.209 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.187 r_nbd_other 0.175 r_symmetry_nbd_refined 0.172 r_symmetry_nbtor_other 0.117 r_symmetry_xyhbond_nbd_other 0.111 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2816 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing