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Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H26 PDB ENTRY 2H26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 1.9 M Ammonium sulfate, 0.2 M Ammonium acetate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.25 α = 90 b = 67.58 β = 112.26 c = 88.19 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 100 CCD MARMOSAIC 225 mm CCD 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 36.54 92.9 0.07 11.2 2.9 81026 81026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 71.1 0.362 1.8 1.6
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 ENTRY 2H26 1.9 20 80866 76823 4044 92.5 0.16719 0.16495 0.1729 0.21075 0.2198 RANDOM 38.89
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] 0.07 0.02 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.081 r_dihedral_angle_4_deg 19.966 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.896 r_scangle_it 5.292 r_scbond_it 3.331 r_angle_refined_deg 2.183 r_mcangle_it 2.14 r_angle_other_deg 1.229 r_mcbond_it 1.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.081 r_dihedral_angle_4_deg 19.966 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.896 r_scangle_it 5.292 r_scbond_it 3.331 r_angle_refined_deg 2.183 r_mcangle_it 2.14 r_angle_other_deg 1.229 r_mcbond_it 1.219 r_mcbond_other 0.372 r_chiral_restr 0.235 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5869 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 376
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling