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Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 400 microliter heptane-triol, 20 microliter 1M Potassium Phosphate pH 6.8, 475mg Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 5.37 77.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.8 α = 90 b = 223.8 β = 90 c = 113.5 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 16M 2021-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 37 100 0.936 4.1 412 151216
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 2.8 2.9 0.529
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 36.8 70965 3534 99.629 0.21 0.215 0.2152 0.253 0.2539 50.965
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] 0.505 0.505 -1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.989 r_dihedral_angle_6_deg 15.113 r_lrange_other 11.424 r_lrange_it 11.421 r_dihedral_angle_2_deg 7.699 r_scangle_it 7.308 r_scangle_other 7.308 r_dihedral_angle_1_deg 7.302 r_mcangle_it 6.635 r_mcangle_other 6.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.989 r_dihedral_angle_6_deg 15.113 r_lrange_other 11.424 r_lrange_it 11.421 r_dihedral_angle_2_deg 7.699 r_scangle_it 7.308 r_scangle_other 7.308 r_dihedral_angle_1_deg 7.302 r_mcangle_it 6.635 r_mcangle_other 6.634 r_scbond_it 4.677 r_scbond_other 4.677 r_mcbond_it 4.33 r_mcbond_other 4.329 r_angle_refined_deg 2.191 r_angle_other_deg 0.583 r_nbd_refined 0.249 r_symmetry_nbd_refined 0.246 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.118 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.061 r_symmetry_xyhbond_nbd_refined 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9346 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 909
Software Software Software Name Purpose MxCuBE data collection CrystFEL data reduction PHASER phasing REFMAC refinement Coot model building