4GHS

Crystal structure of human GLTP bound with 12:0 disulfatide (orthorombic form; two subunits in asymmetric unit)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729810-20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3162.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.948α = 90
b = 94.773β = 90
c = 130.799γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER AXS MICROSTAR2009-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

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
13.25097.9110461075122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3197.9

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3RZN3.214.99101101011051197.920.196620.192750.27616RANDOM33.626
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]
2.74-2.29-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.518
r_dihedral_angle_3_deg21.716
r_dihedral_angle_4_deg21.384
r_dihedral_angle_1_deg7.446
r_scangle_it2.804
r_angle_refined_deg1.919
r_scbond_it1.576
r_mcangle_it1.338
r_angle_other_deg1.071
r_mcbond_it0.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.518
r_dihedral_angle_3_deg21.716
r_dihedral_angle_4_deg21.384
r_dihedral_angle_1_deg7.446
r_scangle_it2.804
r_angle_refined_deg1.919
r_scbond_it1.576
r_mcangle_it1.338
r_angle_other_deg1.071
r_mcbond_it0.704
r_symmetry_vdw_refined0.265
r_symmetry_hbond_refined0.245
r_xyhbond_nbd_refined0.138
r_chiral_restr0.097
r_mcbond_other0.086
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3336
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms106

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling