3NDN

Crystal structure of O-succinylhomoserine sulfhydrylase from Mycobacterium tuberculosis covalently bound to pyridoxal-5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y4I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.528926.9 mg/mL protein against JCSG+ condition A2, 25% PEG 3000, 0.1 M citrate pH 5.5, crystal tracking ID 215797a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5852.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.95α = 90
b = 129.56β = 115.35
c = 95.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.855099.40.06213.564.4154137153275-333.417
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)
11.851.999.60.5292.54.2

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 REPLACEMENTTHROUGHOUT1y4i1.8519.7153169768199.540.1890.1870.223RANDOM39.709
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]
-2.02-1.071.56-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.572
r_dihedral_angle_4_deg15.248
r_dihedral_angle_3_deg13.037
r_dihedral_angle_1_deg5.271
r_scangle_it2.529
r_scbond_it1.512
r_angle_refined_deg1.322
r_mcangle_it0.953
r_mcbond_it0.525
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.572
r_dihedral_angle_4_deg15.248
r_dihedral_angle_3_deg13.037
r_dihedral_angle_1_deg5.271
r_scangle_it2.529
r_scbond_it1.512
r_angle_refined_deg1.322
r_mcangle_it0.953
r_mcbond_it0.525
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12027
Nucleic Acid Atoms
Solvent Atoms1046
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction