3DH7

Structure of T. thermophilus IDI-2 in complex with PPi


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5pH5.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
4.4672.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.528α = 90
b = 142.528β = 90
c = 109.682γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9797ESRFBM30A

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
12.972049971

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.9719.9247599253897.980.215080.210920.29254RANDOM17.776
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_deg39.267
r_dihedral_angle_3_deg26.119
r_dihedral_angle_4_deg22.894
r_dihedral_angle_1_deg10.674
r_scangle_it5.595
r_angle_refined_deg3.098
r_scbond_it3.088
r_mcangle_it2.032
r_mcbond_it1.212
r_nbtor_refined0.351
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.267
r_dihedral_angle_3_deg26.119
r_dihedral_angle_4_deg22.894
r_dihedral_angle_1_deg10.674
r_scangle_it5.595
r_angle_refined_deg3.098
r_scbond_it3.088
r_mcangle_it2.032
r_mcbond_it1.212
r_nbtor_refined0.351
r_nbd_refined0.319
r_symmetry_vdw_refined0.31
r_xyhbond_nbd_refined0.239
r_chiral_restr0.199
r_symmetry_hbond_refined0.157
r_bond_refined_d0.032
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9620
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement