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Crystal structure of the LOV1 Q122N mutant of Klebsormidium nitens phototropin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 Nickel chloride hexahydrate, Tris pH 8.5, lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.93 58.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.878 α = 90 b = 53.878 β = 90 c = 137.406 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 EIGER2 X 9M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918402 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.156 38.098 98.6 0.095 1 21.5 24.4 13135
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 2.156 5.847 98.6 1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.16 38 10780 612 98.462 0.187 0.1845 0.2224 0.2184 45.953
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] 0.416 0.416 -0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.003 r_dihedral_angle_3_deg 16.296 r_lrange_other 10.438 r_lrange_it 10.405 r_scangle_it 9.498 r_scangle_other 9.491 r_dihedral_angle_2_deg 9.226 r_dihedral_angle_1_deg 7.113 r_scbond_it 6.449 r_scbond_other 6.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.003 r_dihedral_angle_3_deg 16.296 r_lrange_other 10.438 r_lrange_it 10.405 r_scangle_it 9.498 r_scangle_other 9.491 r_dihedral_angle_2_deg 9.226 r_dihedral_angle_1_deg 7.113 r_scbond_it 6.449 r_scbond_other 6.448 r_mcangle_it 6.422 r_mcangle_other 6.422 r_mcbond_it 4.877 r_mcbond_other 4.811 r_angle_refined_deg 1.684 r_angle_other_deg 0.561 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.21 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.165 r_nbd_other 0.161 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.024 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 896 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing