4IXZ

Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E6GPDB ENTRY 3E6G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929325.5% PEG 4000, 15% GLYCEROL, 0.17MM LITHIUM SULFATE, 0.085MM TRIS, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.2244.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.817α = 90
b = 86.308β = 90
c = 223.351γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-06-11MSINGLE 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
12.075099.39364211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.1199.3

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 3E6G2.0740.2588708468899.50.1840.1810.247RANDOM23.35
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.752
r_dihedral_angle_4_deg23.611
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg6.957
r_scangle_it4.756
r_scbond_it3.106
r_angle_refined_deg1.972
r_mcangle_it1.758
r_mcbond_it1.08
r_chiral_restr0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.752
r_dihedral_angle_4_deg23.611
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg6.957
r_scangle_it4.756
r_scbond_it3.106
r_angle_refined_deg1.972
r_mcangle_it1.758
r_mcbond_it1.08
r_chiral_restr0.142
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11457
Nucleic Acid Atoms
Solvent Atoms918
Heterogen Atoms22

Software

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