6K90

Pyridoxal Kinase from Leishmania donovani in complex with ADP and Pyridoxamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529516% PEG 8000, 0.1M Sodium Cacodylate, 0.32M Calcium Acetate, 6% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.0941.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.55α = 90
b = 71.41β = 99.07
c = 76.88γ = 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
11.935.79618.37.444075
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94

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 REPLACEMENTTHROUGHOUT1.935.5741827222195.660.175970.174130.20995RANDOM18.01
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]
-0.08-0.10.020.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.917
r_dihedral_angle_4_deg16.147
r_dihedral_angle_3_deg12.514
r_dihedral_angle_1_deg7.158
r_long_range_B_refined4.479
r_long_range_B_other4.432
r_scangle_other3.126
r_mcangle_it2.736
r_mcangle_other2.735
r_scbond_it2.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.917
r_dihedral_angle_4_deg16.147
r_dihedral_angle_3_deg12.514
r_dihedral_angle_1_deg7.158
r_long_range_B_refined4.479
r_long_range_B_other4.432
r_scangle_other3.126
r_mcangle_it2.736
r_mcangle_other2.735
r_scbond_it2.106
r_scbond_other2.089
r_mcbond_it1.859
r_mcbond_other1.852
r_angle_refined_deg1.637
r_angle_other_deg1.459
r_chiral_restr0.08
r_bond_refined_d0.011
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 Atoms4299
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing