6FXW

Structure of Leishmania infantum type B ribose 5-phosphate isomerase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1M Hepes pH7; 2M NH4SO4
Crystal Properties
Matthews coefficientSolvent content
238.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.92α = 90
b = 83.65β = 90
c = 89.49γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.912SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5719.7599.60.052723.26.521306
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.6697.80.3435.09

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 REPLACEMENTTHROUGHOUT3k7o1.5719.7520240106699.550.146110.144390.17829RANDOM17.348
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]
0.280.32-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.657
r_dihedral_angle_4_deg15.196
r_dihedral_angle_3_deg12.162
r_dihedral_angle_1_deg6.22
r_long_range_B_refined5.701
r_long_range_B_other5.691
r_scangle_other4.831
r_scbond_other3.215
r_scbond_it3.21
r_mcangle_other2.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.657
r_dihedral_angle_4_deg15.196
r_dihedral_angle_3_deg12.162
r_dihedral_angle_1_deg6.22
r_long_range_B_refined5.701
r_long_range_B_other5.691
r_scangle_other4.831
r_scbond_other3.215
r_scbond_it3.21
r_mcangle_other2.958
r_mcangle_it2.947
r_angle_refined_deg2.217
r_mcbond_it2.046
r_mcbond_other1.959
r_angle_other_deg1.139
r_chiral_restr0.137
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms1149
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing