3RZN

Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SWX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.127320-25% PEG 8000, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.2645.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.891α = 90
b = 50.06β = 118.52
c = 65.404γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-09-11MSINGLE 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
11.15099.80.0819964622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1599.50.2933.67

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SWX1.114.97281298431299.40.1390.1380.157RANDOM13
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]
-0.14-0.2-0.270.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.63
r_dihedral_angle_3_deg13.997
r_dihedral_angle_4_deg11.758
r_sphericity_free7.385
r_dihedral_angle_1_deg5.196
r_sphericity_bonded4.616
r_scangle_it4.298
r_scbond_it3.318
r_mcangle_it2.308
r_mcbond_it2.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.63
r_dihedral_angle_3_deg13.997
r_dihedral_angle_4_deg11.758
r_sphericity_free7.385
r_dihedral_angle_1_deg5.196
r_sphericity_bonded4.616
r_scangle_it4.298
r_scbond_it3.318
r_mcangle_it2.308
r_mcbond_it2.016
r_angle_other_deg1.881
r_rigid_bond_restr1.713
r_angle_refined_deg1.586
r_mcbond_other0.802
r_symmetry_vdw_other0.246
r_symmetry_vdw_refined0.235
r_nbd_refined0.231
r_symmetry_hbond_refined0.21
r_nbtor_refined0.195
r_nbd_other0.179
r_xyhbond_nbd_refined0.135
r_chiral_restr0.101
r_nbtor_other0.097
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.007
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 Atoms1660
Nucleic Acid Atoms
Solvent Atoms386
Heterogen Atoms61

Software

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