2H2W

Crystal structure of Homoserine O-succinyltransferase (EC 2.3.1.46) (Homoserine O-transsuccinylase) (HTS) (tm0881) from THERMOTOGA MARITIMA at 2.52 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP829310.0% iso-Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8856.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.609α = 90
b = 72.609β = 90
c = 126.913γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102003-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0000ALS8.2.1

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
12.5242.399.90.04618.510.981364370.22
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)
12.522.6199.799.70.3876.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GHR2.5242.31257361392.360.1940.190.274RANDOM44.358
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]
1.980.991.98-2.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.477
r_dihedral_angle_4_deg17.047
r_dihedral_angle_3_deg14.03
r_dihedral_angle_1_deg6.054
r_scangle_it4.237
r_scbond_it3.013
r_mcangle_it2.749
r_mcbond_it1.859
r_angle_refined_deg1.211
r_angle_other_deg0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.477
r_dihedral_angle_4_deg17.047
r_dihedral_angle_3_deg14.03
r_dihedral_angle_1_deg6.054
r_scangle_it4.237
r_scbond_it3.013
r_mcangle_it2.749
r_mcbond_it1.859
r_angle_refined_deg1.211
r_angle_other_deg0.62
r_mcbond_other0.44
r_symmetry_vdw_other0.282
r_symmetry_hbond_refined0.262
r_nbd_refined0.228
r_nbd_other0.217
r_nbtor_refined0.202
r_xyhbond_nbd_refined0.199
r_symmetry_vdw_refined0.093
r_nbtor_other0.093
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2373
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
MolProbitymodel building
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction