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Monomeric L-threonine 3-dehydrogenase from metagenome database (apo 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 Potassium formate
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.386 α = 90 b = 49.319 β = 89.9 c = 113.602 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 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 1.9 113.6 95.7 16.2 5.1 46791
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 1.93 96.5
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 3WMX 1.9 113.6 44434 2345 94.87 0.19225 0.19008 0.1978 0.23328 0.2424 RANDOM 18.291
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 18.933 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_1_deg 7.058 r_long_range_B_refined 5.769 r_long_range_B_other 5.743 r_scangle_other 4.888 r_scbond_it 3.274 r_scbond_other 3.271 r_mcangle_it 2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 18.933 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_1_deg 7.058 r_long_range_B_refined 5.769 r_long_range_B_other 5.743 r_scangle_other 4.888 r_scbond_it 3.274 r_scbond_other 3.271 r_mcangle_it 2.73 r_mcangle_other 2.73 r_mcbond_it 2.023 r_mcbond_other 2.023 r_angle_refined_deg 1.335 r_angle_other_deg 0.733 r_chiral_restr 0.089 r_bond_refined_d 0.01 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 4958 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing