4YMZ

DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X22 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629316% PEG 8000, 1mM Ammonium sulfate, 10mM EDTA, 1mM Sodium azide, 100mM BIS/TRIS
Crystal Properties
Matthews coefficientSolvent content
3.2361.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.758α = 90
b = 103.758β = 90
c = 113.505γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8756.7592.713.311.8588625480922.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.97

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 REPLACEMENTTHROUGHOUT4X221.8756.7552007259392.760.172950.171120.2107RANDOM27.82
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_deg34.676
r_dihedral_angle_4_deg13.87
r_dihedral_angle_3_deg12.606
r_dihedral_angle_1_deg6.229
r_long_range_B_other5.637
r_long_range_B_refined5.636
r_scangle_other4.402
r_scbond_it3.208
r_scbond_other3.206
r_mcangle_other3.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.676
r_dihedral_angle_4_deg13.87
r_dihedral_angle_3_deg12.606
r_dihedral_angle_1_deg6.229
r_long_range_B_other5.637
r_long_range_B_refined5.636
r_scangle_other4.402
r_scbond_it3.208
r_scbond_other3.206
r_mcangle_other3.187
r_mcangle_it3.182
r_mcbond_it2.578
r_mcbond_other2.568
r_angle_refined_deg2.015
r_angle_other_deg0.942
r_chiral_restr0.131
r_bond_refined_d0.021
r_gen_planes_refined0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3739
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing