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Crystal structure of human Glycolipid Transfer Protein complexed with n-hexyl-beta-D-glucoside
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 4.5 293 15-20% PEG 3350, potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.913 α = 90 b = 42.18 β = 104.57 c = 70.819 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 2005-05-30 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 98.6 0.08 8.7 3.9 22940 22940
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 2.28 98.1 0.452 3.9 2236
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 1SWX 2.2 15 22916 22916 1179 98.27 0.192 0.192 0.19 0.1992 0.236 0.1915 RANDOM 35.736
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] 1.21 -0.6 -0.48 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.845 r_dihedral_angle_4_deg 20.571 r_dihedral_angle_3_deg 18.634 r_dihedral_angle_1_deg 5.769 r_scangle_it 2.495 r_scbond_it 1.69 r_angle_other_deg 1.479 r_angle_refined_deg 1.467 r_mcangle_it 1.136 r_mcbond_it 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.845 r_dihedral_angle_4_deg 20.571 r_dihedral_angle_3_deg 18.634 r_dihedral_angle_1_deg 5.769 r_scangle_it 2.495 r_scbond_it 1.69 r_angle_other_deg 1.479 r_angle_refined_deg 1.467 r_mcangle_it 1.136 r_mcbond_it 0.82 r_symmetry_vdw_other 0.231 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.207 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.183 r_nbd_other 0.182 r_mcbond_other 0.167 r_nbtor_other 0.093 r_chiral_restr 0.087 r_xyhbond_nbd_other 0.069 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3166 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction AMoRE phasing