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Crystal structure of human Glycolipid Transfer Protein complexed with 8:0 Lactosylceramide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EUK PDB ENTRY 2EUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 15-20% PEG 3350 or 8000, 50 mM possium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.509 α = 90 b = 49.264 β = 122.57 c = 68.66 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 mirrors 2005-10-28 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 2.3 20 99.9 0.095 3.6 9584 9562
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 2.3 2.38 99.9 0.523 3.4 946
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 2EUK 2.3 20 9584 9562 460 99.9 0.187 0.187 0.184 0.1828 0.25 0.2509 RANDOM 43.892
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] -2.31 -0.58 0.83 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.43 r_dihedral_angle_4_deg 21.085 r_dihedral_angle_3_deg 16.031 r_dihedral_angle_1_deg 5.601 r_scangle_it 2.512 r_scbond_it 1.494 r_angle_refined_deg 1.259 r_mcangle_it 1.196 r_mcbond_it 0.669 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.43 r_dihedral_angle_4_deg 21.085 r_dihedral_angle_3_deg 16.031 r_dihedral_angle_1_deg 5.601 r_scangle_it 2.512 r_scbond_it 1.494 r_angle_refined_deg 1.259 r_mcangle_it 1.196 r_mcbond_it 0.669 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing