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X-ray crystal structure of LsAA9A - cinnamon extract soak
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 4 295 3.5 M NaCl, 0.1 M citric acid pH 4.0.
20-25 mg/ml LsAA9A.
2 ul hanging drops (1:1 protein:reservoir ratio).
Crystal Properties Matthews coefficient Solvent content 3.23 61.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.179 α = 90 b = 125.179 β = 90 c = 125.179 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 PILATUS 6M 2019-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 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 1.45 44.3 100 0.165 0.999 20.57 70.1 59727
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 1.45 1.54 99.8 1.846 0.71 41.3
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 FOURIER SYNTHESIS THROUGHOUT 5ACH 1.45 44.3 56643 3009 99.98 0.1683 0.1672 0.1674 0.1873 0.1869 RANDOM 21.047
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 29.535 r_dihedral_angle_4_deg 11.84 r_dihedral_angle_3_deg 8.61 r_dihedral_angle_1_deg 6.851 r_angle_refined_deg 2.083 r_angle_other_deg 1.584 r_chiral_restr 0.133 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.535 r_dihedral_angle_4_deg 11.84 r_dihedral_angle_3_deg 8.61 r_dihedral_angle_1_deg 6.851 r_angle_refined_deg 2.083 r_angle_other_deg 1.584 r_chiral_restr 0.133 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1788 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction