6LD8

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LD7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52870.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
4.9375.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.985α = 90
b = 161.985β = 90
c = 245.18γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0PAL/PLS5C (4A)

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
12.35099.940.1223.57.3137559
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)
12.312.390.54

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 REPLACEMENTTHROUGHOUT6LD72.3140.61131279694199.950.1670.16550.1945RANDOM32.296
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.965
r_dihedral_angle_4_deg21.729
r_dihedral_angle_3_deg18.047
r_dihedral_angle_1_deg7.376
r_angle_refined_deg1.901
r_angle_other_deg1.459
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.965
r_dihedral_angle_4_deg21.729
r_dihedral_angle_3_deg18.047
r_dihedral_angle_1_deg7.376
r_angle_refined_deg1.901
r_angle_other_deg1.459
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11491
Nucleic Acid Atoms
Solvent Atoms597
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASESphasing