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1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 7.5mg/ml, 0.25M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME;
Screen: Classics II(F12), 0.2M Sodium chloride, 0.1M HEPES (pH 7.5), 25%(w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.845 α = 75.43 b = 84.351 β = 65.97 c = 92.463 γ = 62.03
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 C(111) 2014-06-16 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) R Sym I (Observed) CC (Half) 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 1.65 30 97.1 0.083 0.083 0.757 14.8 3.9 225519 -3 20.1
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 1.65 1.68 95.5 0.622 2.3 3.9
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 3M9Y 1.65 29.69 212575 11243 97.08 0.19796 0.19617 0.2044 0.23154 0.2404 RANDOM 22.805
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] -1.41 0.22 -0.08 0.05 -0.12 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.575 r_dihedral_angle_4_deg 10.791 r_dihedral_angle_3_deg 10.239 r_long_range_B_refined 5.727 r_long_range_B_other 5.393 r_dihedral_angle_1_deg 3.513 r_scangle_other 1.72 r_angle_refined_deg 1.458 r_mcangle_it 1.259 r_mcangle_other 1.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.575 r_dihedral_angle_4_deg 10.791 r_dihedral_angle_3_deg 10.239 r_long_range_B_refined 5.727 r_long_range_B_other 5.393 r_dihedral_angle_1_deg 3.513 r_scangle_other 1.72 r_angle_refined_deg 1.458 r_mcangle_it 1.259 r_mcangle_other 1.259 r_scbond_it 1.106 r_scbond_other 1.106 r_angle_other_deg 0.86 r_mcbond_it 0.806 r_mcbond_other 0.805 r_chiral_restr 0.085 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14787 Nucleic Acid Atoms Solvent Atoms 2372 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing