2V2D

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 1ML1PDB ENTRY 1ML1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.21.75 M (NH4)2PO4, PH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.23α = 90
b = 95.23β = 90
c = 48.82γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHFLAT PRE-MIRROR AND BENT, VERTICALLY FOCUSSING2004-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
12.32599.20.0824.4512.1113213
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)
12.32.3599.90.2213.0312.44

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 1ML12.319.22107555651000.2040.2010.27RANDOM16.92
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]
-1.87-0.94-1.872.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.394
r_dihedral_angle_4_deg18.613
r_dihedral_angle_3_deg17.989
r_dihedral_angle_1_deg6.197
r_scangle_it2.349
r_scbond_it1.632
r_angle_refined_deg1.458
r_mcangle_it0.97
r_mcbond_it0.598
r_symmetry_hbond_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.394
r_dihedral_angle_4_deg18.613
r_dihedral_angle_3_deg17.989
r_dihedral_angle_1_deg6.197
r_scangle_it2.349
r_scbond_it1.632
r_angle_refined_deg1.458
r_mcangle_it0.97
r_mcbond_it0.598
r_symmetry_hbond_refined0.332
r_nbtor_refined0.301
r_nbd_refined0.227
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.166
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms1829
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing