3K7O

Structure of type B ribose 5-phosphate isomerase from Trypanosoma cruzi


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.5% (v/v) Jeffamine ED-2001, 0.1M HEPES, 1.1 M Na-malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.199α = 90
b = 93.199β = 90
c = 93.712γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
1266.08299.70.0780.07813.1528418
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)
122.111000.6410.6411.254075

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT3K7P23027811139897.570.2010.2010.1990.225RANDOM31.092
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.212
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg13.662
r_dihedral_angle_1_deg4.871
r_scangle_it2.793
r_scbond_it1.648
r_mcangle_it1.145
r_angle_refined_deg1.099
r_mcbond_it0.65
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.212
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg13.662
r_dihedral_angle_1_deg4.871
r_scangle_it2.793
r_scbond_it1.648
r_mcangle_it1.145
r_angle_refined_deg1.099
r_mcbond_it0.65
r_nbtor_refined0.296
r_nbd_refined0.19
r_symmetry_vdw_refined0.142
r_xyhbond_nbd_refined0.114
r_symmetry_hbond_refined0.106
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction