3BIA

Tim-4 in complex with sodium potassium tartrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OR7TIM-2 HOMOLOGOUS MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52940.1 M Hepes, 0.8 M potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2862.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.77α = 90
b = 67.77β = 90
c = 129.09γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.052599.90.0630.0639.519.7117181171427.9
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)
2.052.1699.60.3022.515.41643

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 REPLACEMENTTHROUGHOUTTIM-2 HOMOLOGOUS MODEL2.21590094491000.218570.21760.23782RANDOM25.429
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]
1.470.741.47-2.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.837
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg6.64
r_scangle_it2.413
r_scbond_it1.358
r_angle_refined_deg1.103
r_mcangle_it1.054
r_mcbond_it0.551
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.837
r_dihedral_angle_4_deg15.698
r_dihedral_angle_3_deg15.242
r_dihedral_angle_1_deg6.64
r_scangle_it2.413
r_scbond_it1.358
r_angle_refined_deg1.103
r_mcangle_it1.054
r_mcbond_it0.551
r_nbtor_refined0.299
r_nbd_refined0.194
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.109
r_symmetry_hbond_refined0.095
r_metal_ion_refined0.091
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.003
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_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 Atoms864
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing