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Structure of a microbial glycosphingolipid bound to mouse CD1d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AKR PDB ENTRY 2AKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20 % Polyethylene glycol 4000, 0.1 M sodium citrate, 10% isopropanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.295 α = 90 b = 107.661 β = 90 c = 110.699 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 CCD MARRESEARCH 2005-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.95369 SSRL BL9-2
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 1.8 37 99.9 0.078 17.5 3.6 47802 47802
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 1.8 1.85 99.9 0.722 1.7
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 2AKR 1.8 34.14 47800 46570 1230 99.89 0.20915 0.2082 0.2072 0.24253 0.2416 RANDOM 25.285
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_4_deg 22.177 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.969 r_scangle_it 3.861 r_scbond_it 2.485 r_mcangle_it 1.804 r_angle_refined_deg 1.568 r_mcbond_it 1.099 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_4_deg 22.177 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.969 r_scangle_it 3.861 r_scbond_it 2.485 r_mcangle_it 1.804 r_angle_refined_deg 1.568 r_mcbond_it 1.099 r_nbtor_refined 0.305 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.207 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.129 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 2930 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing