☰ Navigation Tabs
CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding
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 6.5 293 0.2 M Zinc Acetate (Salt)
0.1 M Imidazole pH 6.5 (Buffer)
10 %w/v PEG 8000 (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.803 α = 90 b = 82.803 β = 90 c = 263.071 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9786 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 1.97 71.71 98.8 0.527 0.535 0.089 0.996 10.8 35.8 38197
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 1.97 2.08 100 5.857 5.941 0.991 0.417 35.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6T3Y 1.97 69.28 36174 1913 98.77 0.2122 0.2099 0.2196 0.2549 0.2574 RANDOM 32.208
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] 0.18 0.09 0.18 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_4_deg 16.157 r_dihedral_angle_3_deg 14.854 r_dihedral_angle_1_deg 7.402 r_angle_refined_deg 1.644 r_angle_other_deg 1.265 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_4_deg 16.157 r_dihedral_angle_3_deg 14.854 r_dihedral_angle_1_deg 7.402 r_angle_refined_deg 1.644 r_angle_other_deg 1.265 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction