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Structure of Meiothermus ruber Mrub_1259 LOV domain with N- and C-terminal alpha helices (MrLOVe)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-D3PRD8-F1 residues 1-142
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Magnesium acetate tetrahydrate 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.294 α = 90 b = 77.023 β = 90 c = 103.905 γ = 90
Symmetry Space Group P 21 21 21
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 2023-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97919 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 2.038 47.281 93.5 0.2774 0.2977 0.1069 0.993 6.58 7.58 24125
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) 2.038 2.23 77.3 1.8989 2.0173 0.6727 0.468 1.44 8.83 1206
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-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 AF-D3PRD8-F1 2.4 47.281 20778 1031 87.901 0.232 0.2299 0.2328 0.2794 0.2802 28.683
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] 0.809 0.141 -0.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.472 r_dihedral_angle_3_deg 10.887 r_dihedral_angle_2_deg 6.059 r_dihedral_angle_1_deg 5.197 r_lrange_it 4.986 r_lrange_other 4.986 r_scangle_it 3.128 r_scangle_other 3.128 r_mcangle_it 2.994 r_mcangle_other 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.472 r_dihedral_angle_3_deg 10.887 r_dihedral_angle_2_deg 6.059 r_dihedral_angle_1_deg 5.197 r_lrange_it 4.986 r_lrange_other 4.986 r_scangle_it 3.128 r_scangle_other 3.128 r_mcangle_it 2.994 r_mcangle_other 2.994 r_scbond_it 1.886 r_scbond_other 1.884 r_mcbond_it 1.793 r_mcbond_other 1.793 r_angle_refined_deg 1.099 r_angle_other_deg 0.391 r_nbd_other 0.223 r_nbd_refined 0.215 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.047 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4271 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 124
Software Software Software Name Purpose XDS data reduction STARANISO data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing