2EVL

Crystal structure of human Glycolipid Transfer Protein complexed with 18:2 Galactosylceramide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EUKPDB ENTRY 2EUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.529315-20% PEG 3350 or 8000, 50 mM potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.705α = 90
b = 49.312β = 122.56
c = 68.481γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCmirrors2004-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.2201000.0866.64.81091810918
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)
2.22.281000.394.71084

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2EUK2.220109171091752399.870.1860.1860.1830.249RANDOM31.776
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]
-1.980.050.751.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.528
r_dihedral_angle_4_deg19.062
r_dihedral_angle_3_deg14.117
r_dihedral_angle_1_deg5.651
r_scangle_it2.539
r_scbond_it1.701
r_angle_refined_deg1.274
r_mcangle_it1.188
r_angle_other_deg0.887
r_mcbond_it0.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.528
r_dihedral_angle_4_deg19.062
r_dihedral_angle_3_deg14.117
r_dihedral_angle_1_deg5.651
r_scangle_it2.539
r_scbond_it1.701
r_angle_refined_deg1.274
r_mcangle_it1.188
r_angle_other_deg0.887
r_mcbond_it0.807
r_symmetry_hbond_refined0.287
r_symmetry_vdw_refined0.252
r_nbd_refined0.2
r_xyhbond_nbd_refined0.187
r_nbtor_refined0.183
r_nbd_other0.17
r_mcbond_other0.133
r_symmetry_vdw_other0.126
r_nbtor_other0.113
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1648
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms64

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
AMoREphasing