2EVD

Crystal structure of human Glycolipid Transfer Protein complexed with 12:0 Lactosylceramide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EUMPDB ENTRY 2EUM

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
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.592α = 90
b = 49.36β = 122.38
c = 68.632γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2004-12-09MSINGLE 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
12201000.0587.21454914549
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)
122.071000.6026.81446

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 2EUM220145491454973099.840.1810.1810.1780.234RANDOM38.205
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]
-2.25-0.661.120.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.972
r_dihedral_angle_4_deg16.699
r_dihedral_angle_3_deg15.085
r_dihedral_angle_1_deg5.605
r_scangle_it4.142
r_scbond_it2.747
r_mcangle_it1.866
r_angle_refined_deg1.612
r_mcbond_it1.194
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.972
r_dihedral_angle_4_deg16.699
r_dihedral_angle_3_deg15.085
r_dihedral_angle_1_deg5.605
r_scangle_it4.142
r_scbond_it2.747
r_mcangle_it1.866
r_angle_refined_deg1.612
r_mcbond_it1.194
r_nbtor_refined0.316
r_xyhbond_nbd_refined0.21
r_nbd_refined0.208
r_symmetry_hbond_refined0.173
r_symmetry_vdw_refined0.158
r_chiral_restr0.117
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1643
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms71

Software

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