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Crystal structure of LOV1 domain of phototropin from Klebsormidium nitens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289.15 magnesium Sulfate hydrate, HEPES sodium pH 7.0, lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.868 α = 90 b = 53.868 β = 90 c = 137.014 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 100 PIXEL DECTRIS EIGER X 9M 2022-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.88560 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 42.34 99.7 0.99 17.7 6.8 17804
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.855 5 0.79
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 1.855 42.34 17802 904 99.619 0.195 0.1933 0.2035 0.2208 0.2226 39.681
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] -0.067 -0.067 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.828 r_dihedral_angle_3_deg 16.785 r_dihedral_angle_6_deg 16.634 r_lrange_other 10.034 r_lrange_it 10.021 r_scangle_it 8.105 r_scangle_other 8.1 r_dihedral_angle_1_deg 6.562 r_mcangle_it 5.989 r_mcangle_other 5.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.828 r_dihedral_angle_3_deg 16.785 r_dihedral_angle_6_deg 16.634 r_lrange_other 10.034 r_lrange_it 10.021 r_scangle_it 8.105 r_scangle_other 8.1 r_dihedral_angle_1_deg 6.562 r_mcangle_it 5.989 r_mcangle_other 5.985 r_scbond_other 5.375 r_scbond_it 5.369 r_mcbond_it 3.877 r_mcbond_other 3.877 r_angle_refined_deg 1.661 r_angle_other_deg 0.907 r_symmetry_nbd_refined 0.257 r_nbd_other 0.248 r_nbd_refined 0.234 r_symmetry_nbd_other 0.223 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.084 r_gen_planes_other 0.013 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 979 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing