5ZEE

Crystal structure of Entamoeba histolytica Arginase in complex with N(omega)-hydroxy-L-arginine (NOHA) at 1.74 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CEV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.1M bistris propane (pH- 6.5), 0.2M potassium thiocyanate, 22% Peg 6000
Crystal Properties
Matthews coefficientSolvent content
2.0435.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.722α = 90
b = 97.538β = 90
c = 125.067γ = 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
11.7445.1499.40.9912.585.725534739.3
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)
11.741.8497.90.982.1

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 REPLACEMENTTHROUGHOUT1CEV1.7445.1453212209899.340.157150.155710.19266RANDOM39.828
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]
-0.46-2.282.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.226
r_dihedral_angle_4_deg14.5
r_dihedral_angle_3_deg12.757
r_long_range_B_refined8.04
r_long_range_B_other7.975
r_dihedral_angle_1_deg6.202
r_scangle_other6.127
r_scbond_it4.478
r_scbond_other4.474
r_mcangle_it3.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.226
r_dihedral_angle_4_deg14.5
r_dihedral_angle_3_deg12.757
r_long_range_B_refined8.04
r_long_range_B_other7.975
r_dihedral_angle_1_deg6.202
r_scangle_other6.127
r_scbond_it4.478
r_scbond_other4.474
r_mcangle_it3.089
r_mcangle_other3.089
r_mcbond_it2.416
r_mcbond_other2.416
r_angle_refined_deg1.705
r_angle_other_deg0.994
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms4606
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building