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 DROP5.62940.1 M SODIUM CITRATE, 10 % JEFFAMINE, 10 mM FeCl3. PROTEIN PRE-INCUBATED WITH 5 mM 1,2 DICAPROYL-sn-GLYCERO-3-(PHOSPHO-L-SERINE) AND 5 mM CaCl2, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.3863.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.26α = 90
b = 66.26β = 90
c = 139.39γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97925ESRFID23-1

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
12.52599.90.0575.79.31168016799
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)
2.52.641000.1684.410.2

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 REPLACEMENTTHROUGHOUTTIM-2 HOMOLOGOUS MODEL2.515642132199.930.220820.219430.24831RANDOM36.021
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]
1.340.671.34-2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.398
r_dihedral_angle_4_deg18.573
r_dihedral_angle_3_deg14.926
r_dihedral_angle_1_deg6.214
r_rigid_bond_restr6.153
r_scbond_it5.219
r_scangle_it4.125
r_sphericity_free2.58
r_sphericity_bonded2.283
r_mcangle_it1.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.398
r_dihedral_angle_4_deg18.573
r_dihedral_angle_3_deg14.926
r_dihedral_angle_1_deg6.214
r_rigid_bond_restr6.153
r_scbond_it5.219
r_scangle_it4.125
r_sphericity_free2.58
r_sphericity_bonded2.283
r_mcangle_it1.115
r_angle_refined_deg1.114
r_mcbond_it0.64
r_nbtor_refined0.298
r_nbd_refined0.189
r_symmetry_vdw_refined0.165
r_metal_ion_refined0.148
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.11
r_chiral_restr0.074
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms855
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing