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Proline utilization A with the FADH- N5 atom covalently modified by proline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286 CRYSTALLIZATION: 5 mg/mL PROTEIN, 14% (W/V) PEG-3350, 0.2M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYSTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L-PROLINE, 1 mM COENZYME Q1, 1mM NAD+, FOR 24 HRS AND THEN FLASH-COOLED IN LIQUID NITROGEN
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.603 α = 90 b = 102.572 β = 106.47 c = 127.203 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 EIGER X 16M 2022-03-27 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 1.88 121.99 97.2 0.103 0.111 0.042 0.998 12.5 7.1 385647
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 1.88 1.92 87.8 1.173 1.273 0.486 0.534 6.5
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 1.88 67.38 0.31 385647 19297 96.71 0.1714 0.1696 0.1647 0.206 0.2019
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 15.812 f_angle_d 1.06 f_chiral_restr 0.054 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17664 Nucleic Acid Atoms Solvent Atoms 1279 Heterogen Atoms 265
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing