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Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 273 20-25% PEG 8000, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.891 α = 90 b = 50.06 β = 118.52 c = 65.404 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 ADSC QUANTUM 315r 2009-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.1 50 99.8 0.08 19 96462 2
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 1.1 1.15 99.5 0.293 3.67
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1SWX 1.1 14.97 2 81298 4312 99.4 0.139 0.138 0.1475 0.157 0.1673 RANDOM 13
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] -0.14 -0.2 -0.27 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_4_deg 11.758 r_sphericity_free 7.385 r_dihedral_angle_1_deg 5.196 r_sphericity_bonded 4.616 r_scangle_it 4.298 r_scbond_it 3.318 r_mcangle_it 2.308 r_mcbond_it 2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_4_deg 11.758 r_sphericity_free 7.385 r_dihedral_angle_1_deg 5.196 r_sphericity_bonded 4.616 r_scangle_it 4.298 r_scbond_it 3.318 r_mcangle_it 2.308 r_mcbond_it 2.016 r_angle_other_deg 1.881 r_rigid_bond_restr 1.713 r_angle_refined_deg 1.586 r_mcbond_other 0.802 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.21 r_nbtor_refined 0.195 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.101 r_nbtor_other 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1660 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 61
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling