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Human CD1c with ligands in A' and F' channel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.2M Magnesium chloride, 0.1M Tris pH 8, 10% PEG 8000, 1:1 protein to precipitant ratio.
Crystal Properties Matthews coefficient Solvent content 3.44 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.13 α = 90 b = 97.13 β = 90 c = 115.08 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315r 2011-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 28.34 97.8 0.054 0.066 15.39 3.04 46442 -4 -3 52.941
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 84.9 0.599 0.756 1.78
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 3OV6 2.4 28.34 22416 1992 97.55 0.15823 0.15453 0.1582 0.20006 0.2025 RANDOM 61.771
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] -8.85 -8.85 17.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.591 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 15.619 r_long_range_B_refined 9.664 r_long_range_B_other 9.66 r_dihedral_angle_1_deg 8.214 r_scangle_other 7.931 r_mcangle_it 6.138 r_mcangle_other 6.136 r_scbond_it 5.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.591 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 15.619 r_long_range_B_refined 9.664 r_long_range_B_other 9.66 r_dihedral_angle_1_deg 8.214 r_scangle_other 7.931 r_mcangle_it 6.138 r_mcangle_other 6.136 r_scbond_it 5.752 r_scbond_other 5.7 r_mcbond_it 4.608 r_mcbond_other 4.603 r_angle_refined_deg 2.372 r_angle_other_deg 1.188 r_chiral_restr 0.147 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3052 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XSCALE data scaling XDS data reduction