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Structure of a C-terminal deletion mutant of Thermoplasma acidophilum aldohexose dehydrogenase (AldT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTD PDB ENTRY 2DTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M imidazol, 0.8M Na/K tartrate, 0.1M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.238 α = 90 b = 68.238 β = 90 c = 337.356 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 4 2006-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50 99.6 0.106 43.5 18.5 13725 13725 74.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.611 7.9 18.4 1308
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 (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 2DTD 2.71 40.72 12962 662 99.63 0.23979 0.23738 0.2334 0.28911 0.2895 RANDOM 77.567
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] 0.53 0.26 0.53 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_3_deg 17.571 r_dihedral_angle_1_deg 5.663 r_scangle_it 1.137 r_angle_refined_deg 1.133 r_scbond_it 0.696 r_mcangle_it 0.646 r_mcbond_it 0.365 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_3_deg 17.571 r_dihedral_angle_1_deg 5.663 r_scangle_it 1.137 r_angle_refined_deg 1.133 r_scbond_it 0.696 r_mcangle_it 0.646 r_mcbond_it 0.365 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3661 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing