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Revised Crystal Structure of apo-form of Triosephosphate Isomerase (tpiA) from Escherichia coli at 1.8 Angstrom Resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D11), 0.2M Calcium chloride, 0.1M Tris-HCl pH 8.0, 20% (w/v) PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.066 α = 90 b = 67.488 β = 90 c = 149.769 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 Mirrors 2013-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.03326 APS 21-ID-D
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 1.8 30 99.9 0.088 18.3 5.8 44231 44231 -3 18.5
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 1.8 1.83 98.4 0.529 2.6 4.1 2158
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 1TRE 1.8 29.06 41906 41906 2228 99.85 0.15075 0.15075 0.14895 0.1588 0.1847 0.1954 RANDOM 16.865
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] 0.02 -0.16 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 10.237 r_dihedral_angle_3_deg 9.469 r_scangle_it 4.664 r_scbond_it 2.815 r_dihedral_angle_1_deg 2.769 r_mcangle_it 1.584 r_angle_refined_deg 1.327 r_mcbond_it 0.973 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 10.237 r_dihedral_angle_3_deg 9.469 r_scangle_it 4.664 r_scbond_it 2.815 r_dihedral_angle_1_deg 2.769 r_mcangle_it 1.584 r_angle_refined_deg 1.327 r_mcbond_it 0.973 r_angle_other_deg 0.878 r_mcbond_other 0.329 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3786 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 1
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling