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Crystal structure of fatty acid photodecarboxylase in the dark state determined by serial femtosecond crystallography at room temperature
Serial Crystallography (SX)
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 BATCH MODE 5.5 281.15 19% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.5, 10 mM spermidine
Crystal Properties Matthews coefficient Solvent content 2.76 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.39 α = 90 b = 60.01 β = 90.6 c = 182.9 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 277.15 PIXEL CS-PAD CXI-1 2018-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2 25 100 0.982 0.151 5.6 355 93061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.548 0.685 236
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 FREE R-VALUE 6YRU 2 24.95 85938 4364 99.89 0.198 0.1963 0.2031 0.2312 0.2355 RANDOM 29.803
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] 1.13 -1.56 -1.19 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 15.944 r_dihedral_angle_1_deg 7.206 r_angle_refined_deg 1.491 r_angle_other_deg 1.286 r_chiral_restr 0.066 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 15.944 r_dihedral_angle_1_deg 7.206 r_angle_refined_deg 1.491 r_angle_other_deg 1.286 r_chiral_restr 0.066 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8417 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHASER phasing Coot model building