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Crystal structure of human Glycolipid Transfer Protein complexed with 12:0 Lactosylceramide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EUM PDB ENTRY 2EUM
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 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.592 α = 90 b = 49.36 β = 122.38 c = 68.632 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 2004-12-09 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 20 100 0.058 7.2 14549 14549
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 2.07 100 0.602 6.8 1446
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 2EUM 2 20 14549 14549 730 99.84 0.181 0.181 0.178 0.1778 0.234 0.2341 RANDOM 38.205
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] -2.25 -0.66 1.12 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.972 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_1_deg 5.605 r_scangle_it 4.142 r_scbond_it 2.747 r_mcangle_it 1.866 r_angle_refined_deg 1.612 r_mcbond_it 1.194 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.972 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_1_deg 5.605 r_scangle_it 4.142 r_scbond_it 2.747 r_mcangle_it 1.866 r_angle_refined_deg 1.612 r_mcbond_it 1.194 r_nbtor_refined 0.316 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.173 r_symmetry_vdw_refined 0.158 r_chiral_restr 0.117 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1643 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing