3K7P

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NN4pdb entry 1NN4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22930.8 M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.079α = 90
b = 93.079β = 90
c = 93.827γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-10-27MSINGLE 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
11.43098.20.0970.09711.15.779637
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)
11.41.481000.3350.3353.15.711693

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 REPLACEMENTTHROUGHOUTpdb entry 1NN41.43079570397797.780.2230.2230.2230.232RANDOM16.949
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]
0.310.31-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.721
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg11.612
r_dihedral_angle_1_deg4.304
r_scangle_it1.943
r_scbond_it1.2
r_angle_refined_deg0.943
r_mcangle_it0.823
r_mcbond_it0.488
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.721
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg11.612
r_dihedral_angle_1_deg4.304
r_scangle_it1.943
r_scbond_it1.2
r_angle_refined_deg0.943
r_mcangle_it0.823
r_mcbond_it0.488
r_nbtor_refined0.299
r_nbd_refined0.181
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.083
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2340
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms10

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
SCALAdata scaling