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NanoLuc luciferase with bound furimamide in surface allosteric site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B0U 5B0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293.15 200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.91 α = 90 b = 87.489 β = 90.09 c = 191.761 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 2M-F 2021-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9999 SLS X06DA
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 1.69 47.94 99.3 0.066 0.996 9.7 3.4 158483
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 1.69 1.73 0.503
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5B0U 1.69 47.94 148996 7979 97.66 0.1369 0.1345 0.1827 0.2174 RANDOM 31.334
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] 2.54 2.26 9.89 -12.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.056 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_4_deg 13.948 r_dihedral_angle_1_deg 8.706 r_rigid_bond_restr 6.413 r_angle_refined_deg 2.152 r_angle_other_deg 1.397 r_chiral_restr 0.145 r_bond_refined_d 0.016 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.056 r_dihedral_angle_3_deg 17.17 r_dihedral_angle_4_deg 13.948 r_dihedral_angle_1_deg 8.706 r_rigid_bond_restr 6.413 r_angle_refined_deg 2.152 r_angle_other_deg 1.397 r_chiral_restr 0.145 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10800 Nucleic Acid Atoms Solvent Atoms 771 Heterogen Atoms 165
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction