6K91

Pyridoxal Kinase from Leishmania donovani in complex with ADP and Pyridoxine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529517% PEG 8000, 0.1M Sodium Cacodylate, 0.32M Calcium Acetate, 6% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.1141.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.7α = 90
b = 71.69β = 99.28
c = 77.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2018-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
1243.129510.12.937788
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0491.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT243.1235946185294.710.17580.173660.21785RANDOM17.329
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]
0.12-0.150.22-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.456
r_dihedral_angle_4_deg18.36
r_dihedral_angle_3_deg13.011
r_dihedral_angle_1_deg7.045
r_long_range_B_refined4.155
r_long_range_B_other4.051
r_scangle_other2.681
r_mcangle_it2.375
r_mcangle_other2.375
r_scbond_it1.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.456
r_dihedral_angle_4_deg18.36
r_dihedral_angle_3_deg13.011
r_dihedral_angle_1_deg7.045
r_long_range_B_refined4.155
r_long_range_B_other4.051
r_scangle_other2.681
r_mcangle_it2.375
r_mcangle_other2.375
r_scbond_it1.759
r_scbond_other1.728
r_angle_refined_deg1.553
r_mcbond_it1.484
r_mcbond_other1.484
r_angle_other_deg1.406
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms4349
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing