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Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SX6 PDB Entry 1SX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 15-20% PEG 3350 or 8000, 50 mM potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.867 α = 90 b = 49.304 β = 122.61 c = 68.655 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 IV mirror 2004-09-17 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 1.85 20 97.3 0.049 4.1 18350 17855
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) 1.85 1.92 94 0.503 3.4 1709
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 PDB Entry 1SX6 1.85 20 18350 17855 920 97.22 0.183 0.181 0.181 0.1782 0.23 0.2267 RANDOM 32.713
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] -1.9 -0.73 1.21 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_1_deg 5.622 r_scangle_it 4.61 r_scbond_it 3.137 r_mcangle_it 1.996 r_angle_refined_deg 1.841 r_mcbond_it 1.328 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_4_deg 15.724 r_dihedral_angle_1_deg 5.622 r_scangle_it 4.61 r_scbond_it 3.137 r_mcangle_it 1.996 r_angle_refined_deg 1.841 r_mcbond_it 1.328 r_nbtor_refined 0.316 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.213 r_symmetry_vdw_refined 0.171 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1646 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 65
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing