3S0K

Crystal Structure of Human Glycolipid Transfer Protein complexed with glucosylceramide containing oleoyl acyl chain (18:1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.527320-25% PEG 3350 , 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.659α = 90
b = 61.646β = 90
c = 67.214γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273CCDADSC QUANTUM 315r2008-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.45098.20.052411402
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4590.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.41539019209697.70.1520.150.182RANDOM13.93
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]
-0.340.85-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.945
r_dihedral_angle_4_deg14.853
r_dihedral_angle_3_deg12.912
r_sphericity_free8.392
r_dihedral_angle_1_deg5.077
r_scangle_it4.612
r_sphericity_bonded4.143
r_scbond_it3.534
r_mcangle_it2.372
r_rigid_bond_restr2.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.945
r_dihedral_angle_4_deg14.853
r_dihedral_angle_3_deg12.912
r_sphericity_free8.392
r_dihedral_angle_1_deg5.077
r_scangle_it4.612
r_sphericity_bonded4.143
r_scbond_it3.534
r_mcangle_it2.372
r_rigid_bond_restr2.189
r_mcbond_it2.09
r_angle_refined_deg1.721
r_angle_other_deg1.453
r_mcbond_other0.74
r_symmetry_vdw_refined0.32
r_nbd_refined0.245
r_nbtor_refined0.199
r_nbd_other0.183
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_other0.151
r_chiral_restr0.092
r_nbtor_other0.091
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1638
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms52

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling