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The functional role of the conserved active site proline of triosephosphate isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TIM PDB ENTRY 5TIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 WELL 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 coefficient Solvent content 2.07 40.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.5 α = 80.49 b = 43.72 β = 79.61 c = 71.27 γ = 64.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MONTEL MIRRORS 2004-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 25 94.5 0.07 13.8 2.65 22102 17.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 92.2 0.13 8.67 2.63
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5TIM 2.1 19.21 20995 1106 100 0.153 0.149 0.1581 0.23 0.2385 RANDOM 7.11
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] 0.3 0.12 0.21 0.15 -0.79 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.228 r_dihedral_angle_3_deg 16.431 r_dihedral_angle_4_deg 13.964 r_dihedral_angle_1_deg 7.264 r_scangle_it 2.567 r_scbond_it 1.833 r_angle_refined_deg 1.638 r_mcangle_it 1.008 r_angle_other_deg 0.88 r_mcbond_it 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.228 r_dihedral_angle_3_deg 16.431 r_dihedral_angle_4_deg 13.964 r_dihedral_angle_1_deg 7.264 r_scangle_it 2.567 r_scbond_it 1.833 r_angle_refined_deg 1.638 r_mcangle_it 1.008 r_angle_other_deg 0.88 r_mcbond_it 0.792 r_symmetry_vdw_other 0.233 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.201 r_nbd_other 0.192 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.172 r_chiral_restr 0.097 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3762 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing