4IY7

crystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv. oryzae in complex with E-site serine, A-site external aldimine structure with serine and A-site external aldimine structure with aminoacrylate intermediates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IXZPDB ENTRY 4IXZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929325.5% PEG 4000, 0.17M LITHIUM SULFATE, 0.085 TRIS, 15% GLYCEROL, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.219α = 90
b = 86.069β = 90
c = 225.997γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.00000PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.675085.517141311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.799.2

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 4IXZ1.730.2315551782071000.1360.1340.169RANDOM15.26
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.215
r_dihedral_angle_4_deg21.223
r_dihedral_angle_3_deg13.617
r_dihedral_angle_1_deg6.597
r_scangle_it5.693
r_scbond_it3.587
r_angle_refined_deg2.262
r_mcangle_it2.05
r_mcbond_it1.303
r_chiral_restr0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.215
r_dihedral_angle_4_deg21.223
r_dihedral_angle_3_deg13.617
r_dihedral_angle_1_deg6.597
r_scangle_it5.693
r_scbond_it3.587
r_angle_refined_deg2.262
r_mcangle_it2.05
r_mcbond_it1.303
r_chiral_restr0.28
r_bond_refined_d0.03
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11469
Nucleic Acid Atoms
Solvent Atoms1428
Heterogen Atoms144

Software

Software
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling