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monomeric L-threonine 3-dehydrogenase from metagenome database (L-Ser and 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 2.03 39.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.594 α = 90 b = 50.857 β = 105.6 c = 55.252 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 PILATUS 2M 2016-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.10 Photon Factory BL-1A
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 1.9 54.2 98.7 17.2 6.6 23337
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 1.9 1.95
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 1.9 54.22 22187 1150 98.03 0.16022 0.15822 0.1703 0.199 0.2047 RANDOM 19.277
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 16.069 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 7.209 r_long_range_B_other 6.854 r_long_range_B_refined 6.849 r_scangle_other 5.928 r_scbond_it 4.049 r_scbond_other 4.014 r_mcangle_it 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 16.069 r_dihedral_angle_3_deg 15.26 r_dihedral_angle_1_deg 7.209 r_long_range_B_other 6.854 r_long_range_B_refined 6.849 r_scangle_other 5.928 r_scbond_it 4.049 r_scbond_other 4.014 r_mcangle_it 3.09 r_mcangle_other 3.089 r_mcbond_it 2.308 r_mcbond_other 2.292 r_angle_refined_deg 1.489 r_angle_other_deg 0.811 r_chiral_restr 0.211 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 2479 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing