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Minimal PutA proline dehydrogenase domain (design #2) with the FAD N5 modified with propanal resulting from inactivation with N-allylglycine(replicate #1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05 - 0.2 M sodium formate and 19 - 24% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.943 α = 104.29 b = 55.099 β = 100.38 c = 76.057 γ = 108.61
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 EIGER X 16M 2022-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.54 70.71 92.7 0.041 0.049 0.026 0.999 15.2 3.7 96174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 89.1 0.446 0.518 0.263 0.88 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.54 49.36 1.15 96142 4716 92.63 0.1697 0.1686 0.1685 0.1919 0.1918
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 f_dihedral_angle_d 13.862 f_angle_d 0.886 f_chiral_restr 0.048 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5794 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 220
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing