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A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MI5 PDB entry 1MI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 297 0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.2 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.672 α = 90 b = 66.672 β = 90 c = 182.408 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 IMAGE PLATE RIGAKU RAXIS 2004-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 60.86 27619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.65 98.53
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 (All) 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 entry 1MI5 2.6 60.86 26083 1384 98.53 0.21186 0.20955 0.20712 0.2255 0.25572 0.2246 RANDOM 42.008
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] 1.66 0.83 1.66 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.091 r_dihedral_angle_4_deg 18.104 r_dihedral_angle_3_deg 17.011 r_dihedral_angle_1_deg 5.781 r_scangle_it 5.265 r_scbond_it 3.747 r_mcangle_it 2.342 r_mcbond_it 1.661 r_angle_refined_deg 1.197 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.091 r_dihedral_angle_4_deg 18.104 r_dihedral_angle_3_deg 17.011 r_dihedral_angle_1_deg 5.781 r_scangle_it 5.265 r_scbond_it 3.747 r_mcangle_it 2.342 r_mcbond_it 1.661 r_angle_refined_deg 1.197 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7054 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing