3S0I

Crystal Structure of D48V mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo galactosylceramide containing nervonoyl acyl chain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RZN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727320-25% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.0138.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.315α = 90
b = 47.454β = 125.47
c = 63.257γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-11-12MSINGLE 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
11.53099.90.0618.85.1303302
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)
11.51.5599.90.44423.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3RZN1.5153033028748146999.530.156480.154080.20599RANDOM29.447
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]
-0.11-0.090.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.364
r_sphericity_free27.668
r_sphericity_bonded16.513
r_dihedral_angle_3_deg14.264
r_dihedral_angle_4_deg13.73
r_dihedral_angle_1_deg4.872
r_scangle_it4.429
r_scbond_it3.502
r_rigid_bond_restr3.211
r_mcangle_it2.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.364
r_sphericity_free27.668
r_sphericity_bonded16.513
r_dihedral_angle_3_deg14.264
r_dihedral_angle_4_deg13.73
r_dihedral_angle_1_deg4.872
r_scangle_it4.429
r_scbond_it3.502
r_rigid_bond_restr3.211
r_mcangle_it2.435
r_mcbond_it2.108
r_angle_refined_deg1.294
r_mcbond_other0.847
r_symmetry_vdw_refined0.298
r_symmetry_hbond_refined0.28
r_symmetry_vdw_other0.261
r_nbd_refined0.24
r_nbd_other0.193
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.168
r_nbtor_other0.092
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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 Atoms1618
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms61

Software

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