5ZEF

Crystal structure of Entamoeba histolytica Arginase in complex with L- Norvaline at 2.01 A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2293.150.1M bistris propane pH-6.2, 0.2M potassium thiocyanate, 20% Peg 6000
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.947α = 90
b = 98.358β = 90
c = 135.329γ = 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
12.014199.60.9912.85.339225
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)
12.012.0497.50.972.1

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 REPLACEMENTTHROUGHOUT1CEV2.014137164184098.990.180120.178550.21034RANDOM51.554
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]
-0.89-1.662.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.562
r_dihedral_angle_4_deg14.851
r_dihedral_angle_3_deg14.61
r_dihedral_angle_1_deg7.232
r_long_range_B_refined6.827
r_long_range_B_other6.823
r_scangle_other4.372
r_scbond_it3.092
r_scbond_other3.087
r_mcangle_it2.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.562
r_dihedral_angle_4_deg14.851
r_dihedral_angle_3_deg14.61
r_dihedral_angle_1_deg7.232
r_long_range_B_refined6.827
r_long_range_B_other6.823
r_scangle_other4.372
r_scbond_it3.092
r_scbond_other3.087
r_mcangle_it2.813
r_mcangle_other2.813
r_mcbond_it1.938
r_mcbond_other1.934
r_angle_refined_deg1.59
r_angle_other_deg1.075
r_chiral_restr0.128
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms4597
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building