3GVG

Crystal structure of Triosephosphate isomerase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YYApdb entry 1yya, modified with the ccp4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290JCSG+ A3: 200MM (NH4)2H CITRATE, 20% PEG 3350, MYTUD.00317.A AT 30MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3146.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.12α = 90
b = 55.76β = 104.01
c = 76.42γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2009-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
11.5574.1599.50.06413.893.77901878636-322.37
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)
11.551.5998.20.5152.53.45789

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTpdb entry 1yya, modified with the ccp4 program chainsaw1.55207863678636395099.50.1450.1430.169RANDOM14.07
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]
-0.16-0.490.99-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.095
r_dihedral_angle_4_deg15.264
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.633
r_scangle_it4.348
r_scbond_it2.705
r_mcangle_it1.768
r_angle_refined_deg1.7
r_mcbond_it1.053
r_angle_other_deg1.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.095
r_dihedral_angle_4_deg15.264
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.633
r_scangle_it4.348
r_scbond_it2.705
r_mcangle_it1.768
r_angle_refined_deg1.7
r_mcbond_it1.053
r_angle_other_deg1.022
r_mcbond_other0.328
r_chiral_restr0.101
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3778
Nucleic Acid Atoms
Solvent Atoms650
Heterogen Atoms18

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling