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Monomeric L-threonine 3-dehydrogenase from metagenome database (NAD+ bound form)
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 277 20% (w/v) PEG 3350, 0.2M Sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.02 38.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.494 α = 90 b = 48.927 β = 104.71 c = 56.364 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 270 2016-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.25 54.9 91.5 28.9 6.3 75876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28
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 1.25 54.89 72123 3743 91.33 0.15827 0.15709 0.1592 0.18055 0.1812 RANDOM 14.098
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.026 r_dihedral_angle_4_deg 17.639 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 6.78 r_long_range_B_refined 6.585 r_long_range_B_other 6.249 r_scangle_other 4.605 r_scbond_it 3.204 r_scbond_other 3.203 r_mcangle_other 1.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.026 r_dihedral_angle_4_deg 17.639 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 6.78 r_long_range_B_refined 6.585 r_long_range_B_other 6.249 r_scangle_other 4.605 r_scbond_it 3.204 r_scbond_other 3.203 r_mcangle_other 1.893 r_mcangle_it 1.892 r_angle_refined_deg 1.652 r_mcbond_it 1.359 r_mcbond_other 1.349 r_angle_other_deg 0.802 r_chiral_restr 0.271 r_gen_planes_refined 0.015 r_bond_refined_d 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 2499 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing