☰ Navigation Tabs
Split gene transketolase, active alpha2beta2 heterotetramer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 2.1 M DL-malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.078 α = 90 b = 130.047 β = 90 c = 165.897 γ = 90
Symmetry Space Group I 2 2 2
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 2M 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.34 60.878 97.7 0.056 1 16.4 6.1 288149 23.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.36 81.3 1.619 0.266 0.8 3.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1qgd 1.34 60.87 288145 14402 97.584 0.142 0.1409 0.1409 0.1588 0.1588 20.5
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] -0.416 0.42 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.432 r_dihedral_angle_4_deg 20.198 r_dihedral_angle_3_deg 13.682 r_lrange_it 7.705 r_lrange_other 7.705 r_dihedral_angle_1_deg 6.322 r_scangle_it 5.931 r_scangle_other 5.931 r_scbond_it 4.231 r_scbond_other 4.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.432 r_dihedral_angle_4_deg 20.198 r_dihedral_angle_3_deg 13.682 r_lrange_it 7.705 r_lrange_other 7.705 r_dihedral_angle_1_deg 6.322 r_scangle_it 5.931 r_scangle_other 5.931 r_scbond_it 4.231 r_scbond_other 4.227 r_mcangle_it 3.095 r_mcangle_other 3.095 r_angle_other_deg 2.27 r_mcbond_it 2.261 r_mcbond_other 2.26 r_angle_refined_deg 1.534 r_nbd_other 0.277 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.214 r_symmetry_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.206 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.134 r_ncsr_local_group_2 0.093 r_chiral_restr 0.08 r_ncsr_local_group_1 0.078 r_symmetry_nbtor_other 0.065 r_metal_ion_refined 0.048 r_bond_other_d 0.033 r_gen_planes_other 0.013 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8982 Nucleic Acid Atoms Solvent Atoms 1424 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Aimless data scaling MOLREP phasing MoRDa phasing