4GH0

Crystal structure of D48V mutant of human GLTP bound with 12:0 monosulfatide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S0I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529815% PEG 3350, 0.1M MES pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9537.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.984α = 90
b = 47.242β = 125.52
c = 62.193γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-14MSINGLE 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
11.355099.8699544055822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.499.7

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 REPLACEMENTTHROUGHOUT3S0I1.351524040738442196599.790.153590.153590.152150.18078RANDOM20.404
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]
-0.82-0.48-0.080.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.025
r_dihedral_angle_3_deg12.468
r_dihedral_angle_4_deg11.354
r_sphericity_free5.786
r_dihedral_angle_1_deg5.426
r_scangle_it4.229
r_sphericity_bonded4.128
r_scbond_it3.333
r_mcangle_it2.25
r_mcbond_it1.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.025
r_dihedral_angle_3_deg12.468
r_dihedral_angle_4_deg11.354
r_sphericity_free5.786
r_dihedral_angle_1_deg5.426
r_scangle_it4.229
r_sphericity_bonded4.128
r_scbond_it3.333
r_mcangle_it2.25
r_mcbond_it1.911
r_rigid_bond_restr1.839
r_angle_refined_deg1.602
r_angle_other_deg1.273
r_mcbond_other0.729
r_symmetry_vdw_other0.32
r_symmetry_hbond_refined0.233
r_nbd_refined0.222
r_symmetry_vdw_refined0.212
r_nbtor_refined0.192
r_nbd_other0.177
r_xyhbond_nbd_refined0.169
r_chiral_restr0.094
r_nbtor_other0.088
r_xyhbond_nbd_other0.043
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1611
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms64

Software

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