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1.43 Angstrom Resolution Crystal Structure of Triosephosphate Isomerase (tpiA) from Escherichia coli in Complex with Acetyl Phosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TRE PDB ENTRY 1TRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 7.4mg/mL, 0.15M Sodium cloride, 0.01M Tris-HCl pH 8.3;
Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 10mM ACP, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.535 α = 90 b = 67.529 β = 90 c = 150.336 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Beryllium lenses 2013-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.43 30 99.9 0.062 22.7 6.1 88659 88659 -3 16.2
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 1.43 1.45 100 0.534 3.4 6 4416
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1TRE 1.43 29.24 83946 83946 4433 99.91 0.13567 0.13567 0.13456 0.1346 0.15614 0.1556 RANDOM 19.023
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] -0.09 0.66 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 10.242 r_dihedral_angle_3_deg 9.701 r_long_range_B_refined 6.988 r_long_range_B_other 6.384 r_dihedral_angle_1_deg 3.588 r_scangle_other 3.129 r_scbond_it 2.084 r_scbond_other 2.084 r_mcangle_other 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_4_deg 10.242 r_dihedral_angle_3_deg 9.701 r_long_range_B_refined 6.988 r_long_range_B_other 6.384 r_dihedral_angle_1_deg 3.588 r_scangle_other 3.129 r_scbond_it 2.084 r_scbond_other 2.084 r_mcangle_other 2.044 r_mcangle_it 2.043 r_angle_refined_deg 1.471 r_mcbond_it 1.261 r_mcbond_other 1.258 r_angle_other_deg 0.762 r_chiral_restr 0.083 r_gen_planes_refined 0.017 r_gen_planes_other 0.016 r_bond_refined_d 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3780 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 37
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling