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Structure of Meiothermus ruber Mrub_1259 LOV domain (MrLOV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-D3PRD8-F1 residues 15-119
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium sulfate 0.1 M Sodium cacodylate 6.5 30 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 4.31 71.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.593 α = 90 b = 78.593 β = 90 c = 73.381 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 16M 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97918 SSRF BL17UM
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 3.352 44.303 91.1 0.5299 0.5432 0.1174 0.987 5.13 21.69 2991
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.352 3.767 59.4 4.1742 4.2668 0.8687 0.847 1.34 22.9 425
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 3.352 44.303 2991 134 83.292 0.244 0.2422 0.2547 0.2721 0.2655 83.668
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] -0.749 -0.749 1.499
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.524 r_lrange_other 24.513 r_scangle_it 19.433 r_scangle_other 19.419 r_mcangle_it 19.237 r_mcangle_other 19.219 r_mcbond_it 13.027 r_mcbond_other 13.024 r_scbond_it 12.835 r_scbond_other 12.815
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.524 r_lrange_other 24.513 r_scangle_it 19.433 r_scangle_other 19.419 r_mcangle_it 19.237 r_mcangle_other 19.219 r_mcbond_it 13.027 r_mcbond_other 13.024 r_scbond_it 12.835 r_scbond_other 12.815 r_dihedral_angle_3_deg 9.984 r_dihedral_angle_6_deg 6.739 r_dihedral_angle_1_deg 3.352 r_dihedral_angle_2_deg 1.338 r_angle_refined_deg 1.057 r_angle_other_deg 0.315 r_symmetry_nbd_other 0.254 r_symmetry_nbd_refined 0.241 r_nbd_other 0.219 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.04 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.001 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 829 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose XDS data reduction STARANISO data scaling Aimless data scaling REFMAC refinement MOLREP phasing