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Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 100 mM Tris, 200 mM NH4(SO4)2, 25% PEG 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.798 α = 90 b = 106.909 β = 90 c = 110.06 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 1998-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0000 SSRL BL7-1
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 2.8 76.7 98.1 0.056 8.4 4.3 12734 12734 -3 39.3
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 2.8 2.95 96 0.29 2.5 4 1810
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 (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 1CD1 2.8 76.7 11481 11481 1018 98.15 0.22174 0.22174 0.21632 0.2262 0.28097 0.2172 RANDOM 25.724
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] -1.34 -1.16 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 23.189 r_dihedral_angle_3_deg 18.958 r_dihedral_angle_1_deg 7.16 r_scangle_it 1.722 r_angle_refined_deg 1.473 r_scbond_it 0.957 r_mcangle_it 0.773 r_angle_other_deg 0.766 r_mcbond_it 0.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 23.189 r_dihedral_angle_3_deg 18.958 r_dihedral_angle_1_deg 7.16 r_scangle_it 1.722 r_angle_refined_deg 1.473 r_scbond_it 0.957 r_mcangle_it 0.773 r_angle_other_deg 0.766 r_mcbond_it 0.688 r_nbd_refined 0.209 r_symmetry_vdw_other 0.204 r_nbtor_refined 0.189 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.089 r_chiral_restr 0.078 r_mcbond_other 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2987 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 170
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling