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Crystal structure of the LOV1 R60K 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 sodium phosphate monobasic monohydrate, potassium phosphate dibasic at pH 6.9
Crystal Properties Matthews coefficient Solvent content 2.94 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.905 α = 90 b = 53.905 β = 90 c = 137.408 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 PILATUS3 2M 2022-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 1.845 53.905 84.8 0.999 12.7 6.5 15532
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 1.845 5.005 0.999
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 1.845 38.146 12770 668 70.007 0.173 0.1708 0.1816 0.2241 0.2239 34.307
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] -0.016 -0.016 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.348 r_dihedral_angle_6_deg 15.046 r_lrange_it 8.973 r_lrange_other 8.942 r_dihedral_angle_2_deg 8.571 r_scangle_it 7.239 r_scangle_other 7.234 r_dihedral_angle_1_deg 6.854 r_scbond_it 4.867 r_mcangle_it 4.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.348 r_dihedral_angle_6_deg 15.046 r_lrange_it 8.973 r_lrange_other 8.942 r_dihedral_angle_2_deg 8.571 r_scangle_it 7.239 r_scangle_other 7.234 r_dihedral_angle_1_deg 6.854 r_scbond_it 4.867 r_mcangle_it 4.825 r_scbond_other 4.825 r_mcangle_other 4.824 r_mcbond_it 3.532 r_mcbond_other 3.53 r_angle_refined_deg 1.592 r_angle_other_deg 0.528 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_refined 0.236 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.174 r_nbd_other 0.151 r_symmetry_nbd_refined 0.126 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.077 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 962 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing