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Partial Consensus L-threonine 3-dehydrogenase (C-Change)
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 275 20% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate
Crystal Properties Matthews coefficient Solvent content 2.02 38.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.019 α = 90 b = 58.474 β = 92.234 c = 138.13 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 PIXEL DECTRIS PILATUS3 6M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.2 46 99.9 0.074 0.999 16.3 6.8 412432
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 0.559 0.847
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3WMX 2.2 46 60750 3100 99.859 0.211 0.2083 0.2111 0.2582 0.2592 47.019
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] 0.004 0.062 0.075 -0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.584 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 16.304 r_lrange_other 9.261 r_lrange_it 9.254 r_dihedral_angle_1_deg 6.91 r_scangle_it 6.484 r_scangle_other 6.484 r_mcangle_other 6.408 r_mcangle_it 6.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.584 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 16.304 r_lrange_other 9.261 r_lrange_it 9.254 r_dihedral_angle_1_deg 6.91 r_scangle_it 6.484 r_scangle_other 6.484 r_mcangle_other 6.408 r_mcangle_it 6.407 r_mcbond_it 4.507 r_mcbond_other 4.503 r_scbond_it 4.41 r_scbond_other 4.409 r_angle_refined_deg 1.476 r_angle_other_deg 1.27 r_symmetry_xyhbond_nbd_refined 0.351 r_nbd_other 0.251 r_symmetry_xyhbond_nbd_other 0.234 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.162 r_ncsr_local_group_6 0.107 r_ncsr_local_group_4 0.104 r_ncsr_local_group_3 0.102 r_ncsr_local_group_2 0.1 r_ncsr_local_group_1 0.098 r_ncsr_local_group_5 0.098 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9335 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing