3E6G

Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I87PDB ENTRY 2I87

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.528325% PEG3350, 0.2M lithium sulfate monohydrate, 0.1M bis-Tris, pH5.5, sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.6954.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.351α = 90
b = 78.351β = 90
c = 300.989γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702008-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.00000Photon FactoryBL-17A

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
12.8501004444111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2I872.842.264215442154223899.980.219570.219570.215590.29549RANDOM52.296
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.494
r_dihedral_angle_3_deg22.215
r_dihedral_angle_4_deg20.566
r_dihedral_angle_1_deg7.542
r_scangle_it2.955
r_scbond_it1.82
r_angle_refined_deg1.806
r_mcangle_it1.392
r_mcbond_it0.77
r_symmetry_hbond_refined0.428
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.494
r_dihedral_angle_3_deg22.215
r_dihedral_angle_4_deg20.566
r_dihedral_angle_1_deg7.542
r_scangle_it2.955
r_scbond_it1.82
r_angle_refined_deg1.806
r_mcangle_it1.392
r_mcbond_it0.77
r_symmetry_hbond_refined0.428
r_nbtor_refined0.317
r_nbd_refined0.26
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.179
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10559
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms

Software

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