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Crystal structure of L-Threonine bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A1N PDB ENTY 3A1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 50% MPD, 0.1M SODIUM CACODYLATE(PH6.4), 5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.203 α = 90 b = 46.369 β = 113.21 c = 89.751 γ = 90
Symmetry Space Group C 1 2 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 315 2009-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.85 82.479 99.7 0.06 15.4 7.5 48616 17
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 1.85 1.88 99.3 0.269 10 7.5
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 ENTY 3A1N 1.85 30.5 48190 4864 99.1 0.1912 0.1912 0.1921 0.2092 0.1967 RANDOM 21.688
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] 0.01 -0.458 -0.108 0.098
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_improper_angle_d 7.77 c_scangle_it 3.353 c_scbond_it 2.514 c_mcangle_it 2.05 c_angle_deg 1.8 c_mcbond_it 1.55 c_bond_d 0.034 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_improper_angle_d 7.77 c_scangle_it 3.353 c_scbond_it 2.514 c_mcangle_it 2.05 c_angle_deg 1.8 c_mcbond_it 1.55 c_bond_d 0.034 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4982 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling