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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 in P2(1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J16 PDB ENTRY 4J16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Molecular Dimensions MD1-47 Morpheus kit, condition H2: 0.10 M amino acids, 0.1 M pH 6.5 buffers, 30.0% ethylene glycol + PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.53 51.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.075 α = 90 b = 68.866 β = 91.03 c = 132.335 γ = 90
Symmetry Space Group P 1 21 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 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 2.37 132.35 95.22 0.05 0.05 14.5 3.6 79373 75579 46.6
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 2.37 2.54 92 0.366 0.366 2.1 3.3 10491
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 ENTRY 4J16 2.37 132.35 79373 75579 4019 95.22 0.20719 0.20719 0.2047 0.1985 0.25298 0.2478 RANDOM 39.913
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] -0.97 -2.38 2.66 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.524 r_dihedral_angle_3_deg 20.868 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_1_deg 5.552 r_scangle_it 3.43 r_scbond_it 2.021 r_angle_refined_deg 1.394 r_mcangle_it 1.189 r_mcbond_it 0.624 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.524 r_dihedral_angle_3_deg 20.868 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_1_deg 5.552 r_scangle_it 3.43 r_scbond_it 2.021 r_angle_refined_deg 1.394 r_mcangle_it 1.189 r_mcbond_it 0.624 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13813 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 208
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling