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Crystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L7D PDB ENTRY 1L7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 3.5 293 MemStart MemSys kit, condition E2:
0.1M Sodium chloride, 0.1M Na citrate pH 3.5, 0.1M Lithium sulphate, 30% v/v PEG 400, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.44 64.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.318 α = 90 b = 162.318 β = 90 c = 73.883 γ = 120
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 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97949 SSRL BL11-1
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 1.8 140.61 99.52 0.048 0.048 11.3 5 98204 97773 25.81
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 1.8 1.89 97.4 0.437 0.437 1.7 5 15023
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1L7D 1.8 140.61 98204 97733 5210 99.52 0.16754 0.16754 0.16687 0.18024 0.1748 RANDOM 28.759
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.386 r_dihedral_angle_3_deg 19 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_1_deg 5.772 r_scangle_it 4.63 r_scbond_it 2.715 r_mcangle_it 1.66 r_angle_refined_deg 1.525 r_mcbond_it 0.941 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.386 r_dihedral_angle_3_deg 19 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_1_deg 5.772 r_scangle_it 4.63 r_scbond_it 2.715 r_mcangle_it 1.66 r_angle_refined_deg 1.525 r_mcbond_it 0.941 r_chiral_restr 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5452 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 78
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling