2V2C

The A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TIMPDB ENTRY 5TIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M TEA PH 7.5, 2 % PEG 400, 2.0 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
3.3262.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.23α = 90
b = 59.29β = 90
c = 46.95γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMONTEL MIRRORS2005-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.892599.50.0363.268.52272653
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)
11.891.9595.50.0626.986.05

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5TIM1.8920.012589913641000.1420.1390.182RANDOM13.93
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]
0.090.07-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.989
r_dihedral_angle_4_deg16.949
r_dihedral_angle_3_deg14.043
r_dihedral_angle_1_deg6.276
r_scangle_it4.508
r_scbond_it2.829
r_angle_refined_deg1.714
r_mcangle_it1.531
r_mcbond_it1.01
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.989
r_dihedral_angle_4_deg16.949
r_dihedral_angle_3_deg14.043
r_dihedral_angle_1_deg6.276
r_scangle_it4.508
r_scbond_it2.829
r_angle_refined_deg1.714
r_mcangle_it1.531
r_mcbond_it1.01
r_nbtor_refined0.306
r_nbd_refined0.211
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.14
r_symmetry_hbond_refined0.135
r_chiral_restr0.129
r_bond_refined_d0.022
r_gen_planes_refined0.009
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1886
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing