2J24

The functional role of the conserved active site proline of triosephosphate isomerase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17WELL SOLUTION: 0.1 M TEA PH 7.0, 27% PEG 2K MME AND 0.2 M KSCN PROTEIN SOLUTION: 11 MG/ML PROTEIN, 0.02 M TRIS/HCL PH 7.0, 0.1 M NACL, 1 MM DTT, 1 MM EDTA AND 1 MM NAN3.
Crystal Properties
Matthews coefficientSolvent content
2.0740.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.5α = 80.49
b = 43.72β = 79.61
c = 71.27γ = 64.66
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMONTEL MIRRORS2004-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
12.12594.50.0713.82.652210217.7
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)
12.12.292.20.138.672.63

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 5TIM2.119.212099511061000.1530.1490.23RANDOM7.11
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]
0.30.120.210.15-0.79-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.228
r_dihedral_angle_3_deg16.431
r_dihedral_angle_4_deg13.964
r_dihedral_angle_1_deg7.264
r_scangle_it2.567
r_scbond_it1.833
r_angle_refined_deg1.638
r_mcangle_it1.008
r_angle_other_deg0.88
r_mcbond_it0.792
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.228
r_dihedral_angle_3_deg16.431
r_dihedral_angle_4_deg13.964
r_dihedral_angle_1_deg7.264
r_scangle_it2.567
r_scbond_it1.833
r_angle_refined_deg1.638
r_mcangle_it1.008
r_angle_other_deg0.88
r_mcbond_it0.792
r_symmetry_vdw_other0.233
r_symmetry_hbond_refined0.222
r_nbd_refined0.214
r_xyhbond_nbd_refined0.201
r_nbd_other0.192
r_nbtor_refined0.182
r_symmetry_vdw_refined0.172
r_chiral_restr0.097
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3762
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing