3ACZ

Crystal structure of Entamoeba histolytica methionine gamma-lyase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.62771.8M (NH4)2SO4, 0.1M cacodylate buffer, 0.1M Li3(C3H5O(COO)3), 0.1mM pyridozxal 5'-phosphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7955.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.285α = 90
b = 85.336β = 101.96
c = 114.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.975097.60.05822.1153.4129357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.972.0497.10.3883.53.412811

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 REPLACEMENTTHROUGHOUT1.9739.06129283649897.340.1570.1560.19RANDOM26.92
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]
-0.150.08-0.090.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.344
r_dihedral_angle_3_deg15.272
r_dihedral_angle_4_deg14.906
r_dihedral_angle_1_deg5.507
r_scangle_it3.482
r_scbond_it2.205
r_angle_refined_deg1.468
r_mcangle_it1.21
r_mcbond_it0.658
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.344
r_dihedral_angle_3_deg15.272
r_dihedral_angle_4_deg14.906
r_dihedral_angle_1_deg5.507
r_scangle_it3.482
r_scbond_it2.205
r_angle_refined_deg1.468
r_mcangle_it1.21
r_mcbond_it0.658
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11812
Nucleic Acid Atoms
Solvent Atoms1005
Heterogen Atoms72

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling