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Dark state structure of the C432S mutant of Fatty Acid Photodecarboxylase (FAP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 ~ 20-30 % PEG 4000, 0.1 M Citrate pH5.5,
10 mM spermidine
Crystal Properties Matthews coefficient Solvent content 3.17 61.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.375 α = 90 b = 104.683 β = 90 c = 156.179 γ = 90
Symmetry Space Group I 2 2 2
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 2020-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.936 86.956 99.4 0.097 0.998 10.8 3.8 216366 56924 39.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.936 2.05 98.1 0.54 1 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6yru 1.936 46.731 56924 2809 99.38 0.177 0.1752 0.1843 0.2116 0.2169 random selection 36.163
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] 2.656 -0.799 -1.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.696 r_lrange_it 6.479 r_lrange_other 6.437 r_scangle_it 5.361 r_scangle_other 5.361 r_scbond_it 3.724 r_scbond_other 3.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.696 r_lrange_it 6.479 r_lrange_other 6.437 r_scangle_it 5.361 r_scangle_other 5.361 r_scbond_it 3.724 r_scbond_other 3.724 r_mcangle_it 3.447 r_mcangle_other 3.443 r_mcbond_it 2.607 r_mcbond_other 2.602 r_angle_refined_deg 1.649 r_angle_other_deg 1.381 r_nbd_other 0.205 r_nbd_refined 0.201 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4234 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing