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CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M TRIS pH 8.5, 20.0% w/v PEG 4000, 200mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.863 α = 90 b = 60.536 β = 107.88 c = 53.855 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.68 55.9 95 0.097 0.106 0.042 0.997 9.2 6.5 50834
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 1.68 1.77 99.7 1.972 2.138 0.817 0.541 6.7
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 6T3Y 1.68 55.8 48269 2441 94.74 0.2182 0.2164 0.2519 0.2774 RANDOM 35.048
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] 0.02 0.02 -0.15 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.016 r_dihedral_angle_4_deg 17.15 r_dihedral_angle_3_deg 14.044 r_dihedral_angle_1_deg 7.019 r_angle_refined_deg 1.55 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.016 r_dihedral_angle_4_deg 17.15 r_dihedral_angle_3_deg 14.044 r_dihedral_angle_1_deg 7.019 r_angle_refined_deg 1.55 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3064 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction