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Crystal structure of the Pcryo_0617 oxidoreductase/decarboxylase from Psychrobacter cryohalolentis K5 in the presence of NAD and UDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 Protein incubated with 5 mM UDP and 5 mM NAD. Precipitant: 16-20% PEG 5000, 200 mM tetramethylammonium chloride, and 100 mM MES (pH 6)
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.579 α = 90 b = 114.849 β = 90 c = 206.045 γ = 90
Symmetry Space Group P 21 21 21
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 2019-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 97.8 0.081 33.1 5.8 137349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 94.1 0.346 1.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.8 48.95 130428 6921 97.83 0.19844 0.19619 0.2029 0.24067 0.2472 RANDOM 37.058
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_3_deg 15.829 r_long_range_B_refined 7.466 r_long_range_B_other 7.466 r_dihedral_angle_2_deg 6.726 r_dihedral_angle_1_deg 6.578 r_scangle_other 6.055 r_mcangle_it 4.258 r_mcangle_other 4.258 r_scbond_it 4.044 r_scbond_other 4.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.829 r_long_range_B_refined 7.466 r_long_range_B_other 7.466 r_dihedral_angle_2_deg 6.726 r_dihedral_angle_1_deg 6.578 r_scangle_other 6.055 r_mcangle_it 4.258 r_mcangle_other 4.258 r_scbond_it 4.044 r_scbond_other 4.043 r_mcbond_it 3.133 r_mcbond_other 3.133 r_angle_refined_deg 1.427 r_angle_other_deg 0.474 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9669 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 289
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELXDE phasing