2VPS

Structure Of The Bifunctional Leishmania Major Trypanothione Synthetase-Amidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VOBPDB ENTRY 2VOB

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.464

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.05α = 90
b = 85.6β = 90
c = 168.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.752096.50.0921.73.596640
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)
12.752.988.60.463.53.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VOB2.7528.3325883136399.50.2070.2040.25RANDOM53.65
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]
2.92-2.51-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.603
r_dihedral_angle_3_deg18.033
r_dihedral_angle_4_deg17.742
r_dihedral_angle_1_deg9.194
r_scangle_it1.74
r_angle_refined_deg1.464
r_scbond_it1.161
r_angle_other_deg0.902
r_mcangle_it0.847
r_mcbond_it0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.603
r_dihedral_angle_3_deg18.033
r_dihedral_angle_4_deg17.742
r_dihedral_angle_1_deg9.194
r_scangle_it1.74
r_angle_refined_deg1.464
r_scbond_it1.161
r_angle_other_deg0.902
r_mcangle_it0.847
r_mcbond_it0.719
r_symmetry_vdw_other0.298
r_nbd_refined0.217
r_symmetry_vdw_refined0.212
r_nbd_other0.193
r_nbtor_refined0.192
r_symmetry_hbond_refined0.177
r_chiral_restr0.17
r_xyhbond_nbd_refined0.156
r_nbtor_other0.088
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4887
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing