Navigation Tabs Room temperature structure of the dark state of the LOV2 domain of phototropin-2 from Arabidopsis thaliana determined with a serial crystallography approach
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12-17 % PEG8000
0.2 M Calcium acetate
0.1 M MES
Crystal Properties Matthews coefficient Solvent content 1.86 33.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.825 α = 90 b = 40.825 β = 90 c = 133.64 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 4M 2018-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 partial oscillation datasets from 15 crystals fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.2 44.55 100 0.051 0.999 14 87.3 553457 6273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 0.557 0.921 1.9 93.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6QQJ 2.2 19.553 1.34 6231 296 99.33 0.2039 0.2017 0.2 0.2488 0.25
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 f_dihedral_angle_d 11.215 f_angle_d 0.547 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 955 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing
