4GVT

Crystal structure of D48V mutant of human GLTP bound with 12:0 disulfatide (hexagonal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H2Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529810-20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.019α = 90
b = 111.019β = 90
c = 75.206γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9754ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.95096.56872687222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0295.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT4H2Z2.914.8116182587729796.820.197710.197710.193220.28201RANDOM54.335
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]
-0.11-0.06-0.110.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.347
r_dihedral_angle_3_deg21.088
r_dihedral_angle_4_deg12.645
r_dihedral_angle_1_deg6.972
r_scangle_it2.358
r_angle_refined_deg1.713
r_scbond_it1.463
r_mcangle_it1.011
r_angle_other_deg0.956
r_mcbond_it0.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.347
r_dihedral_angle_3_deg21.088
r_dihedral_angle_4_deg12.645
r_dihedral_angle_1_deg6.972
r_scangle_it2.358
r_angle_refined_deg1.713
r_scbond_it1.463
r_mcangle_it1.011
r_angle_other_deg0.956
r_mcbond_it0.849
r_nbd_refined0.248
r_nbtor_refined0.204
r_nbd_other0.192
r_symmetry_vdw_other0.175
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.11
r_mcbond_other0.094
r_nbtor_other0.093
r_chiral_restr0.087
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1659
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

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