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Crystal structure of human Glycolipid Transfer Protein complexed with 18:2 Galactosylceramide
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 potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.705 α = 90 b = 49.312 β = 122.56 c = 68.481 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 2004-09-15 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 2.2 20 100 0.086 6.6 4.8 10918 10918
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) 2.2 2.28 100 0.39 4.7 1084
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 2.2 20 10917 10917 523 99.87 0.186 0.186 0.183 0.1875 0.249 0.2542 RANDOM 31.776
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] -1.98 0.05 0.75 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.528 r_dihedral_angle_4_deg 19.062 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 5.651 r_scangle_it 2.539 r_scbond_it 1.701 r_angle_refined_deg 1.274 r_mcangle_it 1.188 r_angle_other_deg 0.887 r_mcbond_it 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.528 r_dihedral_angle_4_deg 19.062 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 5.651 r_scangle_it 2.539 r_scbond_it 1.701 r_angle_refined_deg 1.274 r_mcangle_it 1.188 r_angle_other_deg 0.887 r_mcbond_it 0.807 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.183 r_nbd_other 0.17 r_mcbond_other 0.133 r_symmetry_vdw_other 0.126 r_nbtor_other 0.113 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing