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Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IZH PDB ENTRIES 4IZH, 1PNO experimental model PDB 1PNO PDB ENTRIES 4IZH, 1PNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Molecular Dimensions MD1-47 Morpheus kit, condition E2: 0.12 M ethylene glycols, 0.1 M pH 6.5 buffers, 30% ethylene glycol + PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.616 α = 90 b = 75.038 β = 90 c = 198.144 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 ADSC QUANTUM 315r Rh coated flat mirror 2011-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.18076 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 39.98 96.29 0.036 0.036 18.4 3.7 38049 36638 62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 79.1 0.557 0.557 1.4 2.6 4538
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 ENTRIES 4IZH, 1PNO 2.41 39.98 38049 36638 1924 96.29 0.20331 0.20331 0.20062 0.1994 0.25328 0.2543 RANDOM 73.164
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] 0.19 0.13 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.919 r_dihedral_angle_3_deg 19.609 r_dihedral_angle_4_deg 16.765 r_dihedral_angle_1_deg 5.391 r_angle_refined_deg 1.106 r_angle_other_deg 0.771 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.919 r_dihedral_angle_3_deg 19.609 r_dihedral_angle_4_deg 16.765 r_dihedral_angle_1_deg 5.391 r_angle_refined_deg 1.106 r_angle_other_deg 0.771 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6906 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 159
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling