4S1H

Pyridoxal kinase of Entamoeba histolytica with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527315% Peg4000, 100mM Tris pH7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.256α = 89.94
b = 44.272β = 102.89
c = 75.246γ = 107.03
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.953ESRFBM14

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
11.65089.80.06829.34363103-3
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)
11.61.6348.50.233.672.21693

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 REPLACEMENTTHROUGHOUTNative Pyridoxal Kinase from Entamoeba histolytica1.65059902316089.630.18880.187220.21894RANDOM26.471
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]
-0.580.60.27-1.51-0.081.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.141
r_dihedral_angle_4_deg16.817
r_dihedral_angle_3_deg12.378
r_long_range_B_other10.923
r_long_range_B_refined10.885
r_scangle_other9.624
r_scbond_it8.117
r_scbond_other8.116
r_dihedral_angle_1_deg6.288
r_mcangle_it5.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.141
r_dihedral_angle_4_deg16.817
r_dihedral_angle_3_deg12.378
r_long_range_B_other10.923
r_long_range_B_refined10.885
r_scangle_other9.624
r_scbond_it8.117
r_scbond_other8.116
r_dihedral_angle_1_deg6.288
r_mcangle_it5.511
r_mcangle_other5.51
r_mcbond_it4.72
r_mcbond_other4.718
r_angle_refined_deg1.548
r_angle_other_deg1.267
r_chiral_restr0.11
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms4426
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms58

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling