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Thiamine Pyrophosphate Bound Transketolase from Lactobacillus salivarius at 2.2A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C7V PDB ENTRY 4C7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 15% W/V PEG3350, 0.1 M SODIUM ACETATE, 0.1 M BIS-TRIS PROPANE PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.99 α = 90 b = 74.99 β = 90 c = 192.85 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M MIRRORS 2012-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.29 53.87 100 0.12 15 9.7 29191
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 2.29 2.35 100 0.68 3.5 10.2
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 4C7V 2.29 45.69 27657 1479 99.92 0.15775 0.15378 0.1607 0.23565 0.2386 RANDOM 33.896
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] -0.17 -0.17 -0.17 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 16.298 r_dihedral_angle_3_deg 16.162 r_dihedral_angle_1_deg 6.56 r_long_range_B_refined 5.554 r_long_range_B_other 5.535 r_scangle_other 4.318 r_mcangle_it 3.044 r_mcangle_other 3.044 r_scbond_it 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 16.298 r_dihedral_angle_3_deg 16.162 r_dihedral_angle_1_deg 6.56 r_long_range_B_refined 5.554 r_long_range_B_other 5.535 r_scangle_other 4.318 r_mcangle_it 3.044 r_mcangle_other 3.044 r_scbond_it 2.861 r_scbond_other 2.861 r_mcbond_it 2.214 r_mcbond_other 2.214 r_angle_refined_deg 1.857 r_angle_other_deg 0.895 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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 5092 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling MOLREP phasing