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LsAA9_A chemically reduced with ascorbic acid (high X-ray dose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ACH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 3.5 M sodium chloride, 0.1 M citric acid pH 4.0
After the crystals were grown, they were transferred to a drop consisting of 3.5 M sodium chloride, 0.1 M citric acid pH 5.5, 0.01 M ascorbic acid pH 5.5 for 20 minutes before flash freezing
Crystal Properties Matthews coefficient Solvent content 3.25 62.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.41 α = 90 b = 125.41 β = 90 c = 125.41 γ = 90
Symmetry Space Group P 41 3 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 EIGER2 X 16M 2020-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.97 PETRA III, DESY P11
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 1.5 44.38 100 0.162 0.999 16.65 20.48 54321
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 2.752 0.597 2.27 21.19
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5ACH 1.5 44.38 51561 2753 99.98 0.1884 0.1874 0.207 0.2131 RANDOM 19.257
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 r_dihedral_angle_2_deg 30.629 r_dihedral_angle_4_deg 11.525 r_dihedral_angle_3_deg 9.248 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.769 r_angle_other_deg 1.427 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.629 r_dihedral_angle_4_deg 11.525 r_dihedral_angle_3_deg 9.248 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.769 r_angle_other_deg 1.427 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1788 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 18
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing