3K8C

Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with 4-deoxy-4-phospho-D-erythronohydroxamic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829320% (w/v) PEG 6000, 0.2 M ammonium chloride, 0.1 M Tris-HCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5652.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.387α = 90
b = 92.387β = 90
c = 94.007γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.165.938960.0970.09714.74.723175
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2195.90.4510.4511.34

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 REPLACEMENTTHROUGHOUT3K7P2.13021960119495.080.218590.216740.25336RANDOM21.7
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]
0.670.67-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.429
r_dihedral_angle_4_deg19.511
r_dihedral_angle_3_deg14.353
r_dihedral_angle_1_deg5.562
r_scangle_it3.524
r_scbond_it2.335
r_mcangle_it1.976
r_angle_refined_deg1.396
r_mcbond_it1.142
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.429
r_dihedral_angle_4_deg19.511
r_dihedral_angle_3_deg14.353
r_dihedral_angle_1_deg5.562
r_scangle_it3.524
r_scbond_it2.335
r_mcangle_it1.976
r_angle_refined_deg1.396
r_mcbond_it1.142
r_nbtor_refined0.294
r_symmetry_hbond_refined0.225
r_nbd_refined0.195
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.18
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.004
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 Atoms2332
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms28

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction