3K7S

Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose 5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP929320% (w/v) PEG 550 monomethyl ether, 0.1 M NaCl, 0.1 M Bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.302α = 90
b = 92.302β = 90
c = 93.584γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.993.65999.363050
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)
11.9299.10.2942.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3K7O1.940630153203990.1720.170.19617.18
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]
0.160.33-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg11.38
r_dihedral_angle_1_deg4.75
r_scangle_it2.343
r_scbond_it1.398
r_angle_refined_deg1.088
r_mcangle_it0.841
r_mcbond_it0.502
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg11.38
r_dihedral_angle_1_deg4.75
r_scangle_it2.343
r_scbond_it1.398
r_angle_refined_deg1.088
r_mcangle_it0.841
r_mcbond_it0.502
r_nbtor_refined0.3
r_symmetry_vdw_refined0.221
r_nbd_refined0.194
r_xyhbond_nbd_refined0.122
r_chiral_restr0.074
r_symmetry_hbond_refined0.06
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4664
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms56

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing