Navigation Tabs Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.6 α = 90 b = 157.12 β = 90 c = 202.74 γ = 90
Symmetry Space Group C 2 2 21
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 4M 2022-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
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) 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 2.3 97.78 100 0.9943 0.0952 7.96 770 112061
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 2.3 2.382 100 0.9523 0.2388 3.66 528
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 2.3 97.78 111898 5444 99.893 0.183 0.1811 0.19 0.2274 0.23 25.303
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] 0.206 0.652 -0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.912 r_dihedral_angle_3_deg 13.956 r_dihedral_angle_2_deg 10.485 r_lrange_it 7.989 r_lrange_other 7.977 r_dihedral_angle_1_deg 7.886 r_scangle_it 6.528 r_scangle_other 6.528 r_mcangle_it 4.745 r_mcangle_other 4.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.912 r_dihedral_angle_3_deg 13.956 r_dihedral_angle_2_deg 10.485 r_lrange_it 7.989 r_lrange_other 7.977 r_dihedral_angle_1_deg 7.886 r_scangle_it 6.528 r_scangle_other 6.528 r_mcangle_it 4.745 r_mcangle_other 4.745 r_scbond_other 4.216 r_scbond_it 4.215 r_mcbond_it 3.146 r_mcbond_other 3.146 r_angle_refined_deg 2.149 r_angle_other_deg 1.034 r_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.16 r_symmetry_nbd_other 0.138 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.123 r_symmetry_nbd_refined 0.103 r_nbd_other 0.091 r_ncsr_local_group_3 0.081 r_ncsr_local_group_5 0.077 r_ncsr_local_group_9 0.07 r_ncsr_local_group_12 0.07 r_symmetry_nbtor_other 0.068 r_ncsr_local_group_2 0.068 r_ncsr_local_group_6 0.068 r_ncsr_local_group_7 0.066 r_ncsr_local_group_11 0.065 r_ncsr_local_group_4 0.064 r_ncsr_local_group_1 0.062 r_ncsr_local_group_8 0.061 r_ncsr_local_group_10 0.057 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17873 Nucleic Acid Atoms Solvent Atoms 995 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing
