5CSS

Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CSR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52970.6 M sodium chloride, 9% PEG 6000, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1743.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.633α = 90
b = 84.079β = 90
c = 143.539γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2013-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.1Photon FactoryBL-1A

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
12.175099.920.96.247245

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5CSR2.175044788239199.660.185160.183080.2245RANDOM34.162
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]
-1.270.780.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.335
r_dihedral_angle_4_deg17.541
r_dihedral_angle_3_deg13.843
r_long_range_B_refined8.564
r_long_range_B_other8.564
r_scangle_other6.548
r_dihedral_angle_1_deg5.638
r_mcangle_it4.24
r_mcangle_other4.24
r_scbond_it4.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.335
r_dihedral_angle_4_deg17.541
r_dihedral_angle_3_deg13.843
r_long_range_B_refined8.564
r_long_range_B_other8.564
r_scangle_other6.548
r_dihedral_angle_1_deg5.638
r_mcangle_it4.24
r_mcangle_other4.24
r_scbond_it4.152
r_scbond_other4.152
r_mcbond_it2.849
r_mcbond_other2.848
r_angle_refined_deg1.55
r_angle_other_deg1.425
r_chiral_restr0.081
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6640
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing