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Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% PEG3350, 0.2M potassium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.556 α = 90 b = 112.694 β = 93.67 c = 92.896 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 MARMOSAIC 225 mm CCD 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 92.7 99.9 0.087 32.5 7.4 73459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.7 0.428 5.6
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 3WMX 2.1 92.7 69820 3612 99.84 0.19491 0.19278 0.1992 0.23513 0.2418 RANDOM 36.065
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.906 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 17.589 r_long_range_B_refined 9.365 r_long_range_B_other 9.365 r_dihedral_angle_1_deg 7.63 r_scangle_other 7.312 r_mcangle_it 5.559 r_mcangle_other 5.558 r_scbond_it 5.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.906 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 17.589 r_long_range_B_refined 9.365 r_long_range_B_other 9.365 r_dihedral_angle_1_deg 7.63 r_scangle_other 7.312 r_mcangle_it 5.559 r_mcangle_other 5.558 r_scbond_it 5.079 r_scbond_other 5.079 r_mcbond_it 3.982 r_mcbond_other 3.982 r_angle_refined_deg 1.2 r_angle_other_deg 1.055 r_chiral_restr 0.095 r_gen_planes_refined 0.015 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9750 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing