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Crystal structure of human Glycolipid Transfer protein in lactosylceramide-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SWX PDB ENTRY 1SWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 PEG 8000, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.599 α = 90 b = 49.073 β = 122.52 c = 68.538 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 IMAGE PLATE RIGAKU RAXIS HTC mirrors 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.9 100 99.6 0.117 15 4.33 16853 16786
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 1.9 1.97 0.49 1.7 1672
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 (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 PDB ENTRY 1SWX 1.95 20 14761 785 99.78 0.1947 0.19479 0.19202 0.1991 0.24429 0.2478 RANDOM 38.691
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] -2.33 -0.23 1.27 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.398 r_scangle_it 3.135 r_scbond_it 1.821 r_mcangle_it 1.316 r_angle_refined_deg 1.24 r_angle_other_deg 0.845 r_mcbond_it 0.701 r_symmetry_hbond_refined 0.376 r_symmetry_vdw_refined 0.263 r_nbd_other 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.398 r_scangle_it 3.135 r_scbond_it 1.821 r_mcangle_it 1.316 r_angle_refined_deg 1.24 r_angle_other_deg 0.845 r_mcbond_it 0.701 r_symmetry_hbond_refined 0.376 r_symmetry_vdw_refined 0.263 r_nbd_other 0.218 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_other 0.138 r_nbtor_other 0.088 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction SCALEPACK data scaling AMoRE phasing