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New antiparallel dimer of aureochrome 1a LOV domain mutants from Phaeodactylum tricornutum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.15 in 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2003 under dark conditions
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.746 α = 90 b = 100.746 β = 90 c = 120.57 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS EIGER X 16M 2019-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 46.52 99.96 0.01232 0.01742 0.01232 1 24.51 2 49476 38.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 100 0.2919 0.4128 0.2919 0.838 0.2919 2.39 2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5a8b 1.9 46.52 46990 2486 99.91 0.1538 0.1553 0.1748 0.1753 RANDOM 44.958
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] -0.89 -0.89 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.033 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 13.108 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.652 r_angle_other_deg 1.461 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.033 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 13.108 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.652 r_angle_other_deg 1.461 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2205 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction REFMAC refinement XDS data scaling MOLREP phasing