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Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7Y PDB ENTRIES 2Q7Y AND 2BDN experimental model PDB 2BDN PDB ENTRIES 2Q7Y AND 2BDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 12% PEG3350, 4% v/v Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.3 71.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.948 α = 90 b = 234.948 β = 90 c = 99.172 γ = 120
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 325 mm CCD 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.979 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 37.89 100 0.086 9.3 3.2 56814 56798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 100 0.549 9.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRIES 2Q7Y AND 2BDN 3.1 37.89 56814 53899 2897 99.9 0.20346 0.20199 0.1921 0.23048 0.2187 RANDOM 66.097
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 -0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_4_deg 13.668 r_dihedral_angle_1_deg 5.505 r_angle_refined_deg 1.057 r_scangle_it 0.664 r_scbond_it 0.356 r_mcangle_it 0.196 r_mcbond_it 0.095 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_4_deg 13.668 r_dihedral_angle_1_deg 5.505 r_angle_refined_deg 1.057 r_scangle_it 0.664 r_scbond_it 0.356 r_mcangle_it 0.196 r_mcbond_it 0.095 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12696 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 192
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling