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Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HZZ pdb entry 1HZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 16-20% 8K-PEG, 20-150 mM (NH4)2SO4, 100 mM Mes, pH 6.0 and 10% glycerol in the presence of 50 mM NAD+ and 5 mM NADP+, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.13 α = 90 b = 70.33 β = 90 c = 195.14 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 4 2004-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.933 ESRF ID14-4
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 2.6 47.7 98.5 0.117 0.117 11.4 4.9 27222 27222 2 41.29
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) 2.6 2.74 92.1 0.442 0.442 2.2 2.8 3653
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1HZZ 2.6 41.3 2 25781 25781 1381 98.54 0.25328 0.25328 0.25059 0.2492 0.30388 0.3054 RANDOM 48.122
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] 2.51 -1.53 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.773 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_1_deg 5.213 r_angle_refined_deg 1.163 r_angle_other_deg 0.849 r_mcangle_it 0.681 r_scangle_it 0.56 r_mcbond_it 0.394 r_scbond_it 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.773 r_dihedral_angle_4_deg 14.477 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_1_deg 5.213 r_angle_refined_deg 1.163 r_angle_other_deg 0.849 r_mcangle_it 0.681 r_scangle_it 0.56 r_mcbond_it 0.394 r_scbond_it 0.338 r_symmetry_vdw_other 0.184 r_nbd_refined 0.18 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.161 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.145 r_nbtor_other 0.083 r_xyhbond_nbd_other 0.061 r_chiral_restr 0.058 r_mcbond_other 0.025 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6468 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling EPMR phasing