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Structure of homodimeric luciferase from Enhygromyxa salina
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350 25%, lithium sulfate 0.2 M, BIS-TRIS 0.1 M pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.821 α = 88.72 b = 73.374 β = 77.93 c = 93.972 γ = 87.1
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 S 16M 2021-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9762 ESRF ID23-1
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 2.71 91.89 97 0.068 0.096 0.068 0.981 4 1.8 35543
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) 1 2.71 2.84 96.2 0.218 0.308 0.218 0.894 1.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.71 91.89 33799 1743 97.06 0.19478 0.19096 0.197 0.26877 0.2687 RANDOM 38.378
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] 0.67 1.4 2.21 -0.77 -0.66 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.994 r_dihedral_angle_2_deg 16.545 r_dihedral_angle_1_deg 8.731 r_long_range_B_refined 6.401 r_long_range_B_other 6.394 r_scangle_other 4.336 r_mcangle_it 3.847 r_mcangle_other 3.846 r_scbond_it 2.629 r_scbond_other 2.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.994 r_dihedral_angle_2_deg 16.545 r_dihedral_angle_1_deg 8.731 r_long_range_B_refined 6.401 r_long_range_B_other 6.394 r_scangle_other 4.336 r_mcangle_it 3.847 r_mcangle_other 3.846 r_scbond_it 2.629 r_scbond_other 2.609 r_mcbond_it 2.346 r_mcbond_other 2.344 r_angle_refined_deg 0.338 r_angle_other_deg 0.144 r_chiral_restr 0.02 r_bond_other_d 0.002 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10876 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing