5ZEH

Crystal structure of Entamoeba histolytica Arginase in complex with L- Ornithine at 2.35 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.3293.150.1M bistris propane (pH-9.3), 0.2M potassium thiocyanate, 21% Peg6000
Crystal Properties
Matthews coefficientSolvent content
2.1743.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.605α = 90
b = 97.494β = 90
c = 133.255γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 1M2017-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976251ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.3578.6896.40.996.85.122967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4490.80.672.24.1

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 REPLACEMENTTHROUGHOUT2.3678.6821808115295.770.220820.218630.2623RANDOM72.678
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]
1.74-1.910.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.476
r_dihedral_angle_3_deg14.718
r_dihedral_angle_4_deg11.82
r_dihedral_angle_1_deg6.73
r_long_range_B_refined4.336
r_long_range_B_other4.336
r_angle_refined_deg1.357
r_angle_other_deg0.942
r_mcangle_other0.656
r_mcangle_it0.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.476
r_dihedral_angle_3_deg14.718
r_dihedral_angle_4_deg11.82
r_dihedral_angle_1_deg6.73
r_long_range_B_refined4.336
r_long_range_B_other4.336
r_angle_refined_deg1.357
r_angle_other_deg0.942
r_mcangle_other0.656
r_mcangle_it0.655
r_scangle_other0.478
r_mcbond_it0.364
r_mcbond_other0.361
r_scbond_it0.261
r_scbond_other0.26
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4569
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building