3AEO

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing methionine alpha, beta-enamine-pyridoxamine-5'-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ACZPDB ENTRY 3ACZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.62771.8 M (NH4)2SO4, 0.1 M cacodylate buffer, 0.1 M Li3(C3H5O(COO)3), 0.1 mM pyridozxal 5'-phosphate, pH 6.6, vapor diffusion, sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8356.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.057α = 90
b = 85.703β = 101.39
c = 115.135γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00000SPring-8BL41XU

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
12.155099.90.08913.4713.8102025
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)
2.152.231000.3963.4873.810126

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ACZ2.1539.9101969511098.480.1550.1530.194RANDOM36.66
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]
0.04-0.190.03-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.982
r_dihedral_angle_3_deg16.377
r_dihedral_angle_4_deg16.185
r_dihedral_angle_1_deg5.77
r_scangle_it3.753
r_scbond_it2.352
r_angle_refined_deg1.484
r_mcangle_it1.291
r_mcbond_it0.697
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.982
r_dihedral_angle_3_deg16.377
r_dihedral_angle_4_deg16.185
r_dihedral_angle_1_deg5.77
r_scangle_it3.753
r_scbond_it2.352
r_angle_refined_deg1.484
r_mcangle_it1.291
r_mcbond_it0.697
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11752
Nucleic Acid Atoms
Solvent Atoms736
Heterogen Atoms128

Software

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