2EVT

Crystal structure of D48V mutant of human Glycolipid Transfer Protein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293PEG, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.459α = 90
b = 35.36β = 116.47
c = 58.011γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS HTCmirrors2004-07-20MSINGLE 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
11.992098.10.10418.73.51358813588
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)
11.992.0794.60.4983.41298

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 1SWX1.9920135881358767897.270.2030.2030.2010.255RANDOM30.389
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]
0.060.33-1.211.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.258
r_scangle_it2.594
r_scbond_it1.487
r_angle_other_deg1.171
r_angle_refined_deg1.12
r_mcangle_it1.041
r_mcbond_it0.534
r_symmetry_hbond_refined0.225
r_nbd_other0.22
r_symmetry_vdw_other0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.258
r_scangle_it2.594
r_scbond_it1.487
r_angle_other_deg1.171
r_angle_refined_deg1.12
r_mcangle_it1.041
r_mcbond_it0.534
r_symmetry_hbond_refined0.225
r_nbd_other0.22
r_symmetry_vdw_other0.22
r_nbd_refined0.191
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.162
r_nbtor_other0.098
r_chiral_restr0.056
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1619
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms6

Software

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