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NanoLuc luciferase with bound coelenteramide in surface allosteric site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AQ6 8AQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293.15 MgCl2, KCl, Na acetate, PEG-400
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.979 α = 90 b = 87.282 β = 90.06 c = 191.522 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 1 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 1.99 47.88 98.9 0.087 0.997 8.7 3.3 96944
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 1.99 2.03 0.36
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8AQ6 1.99 44.35 91015 4918 98.19 0.1894 0.1884 0.2006 0.2074 0.22 RANDOM 34.215
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] 3.73 4.15 12.55 -16.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 20.531 r_dihedral_angle_4_deg 14.147 r_dihedral_angle_1_deg 9.608 r_angle_refined_deg 2.246 r_angle_other_deg 1.361 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 20.531 r_dihedral_angle_4_deg 14.147 r_dihedral_angle_1_deg 9.608 r_angle_refined_deg 2.246 r_angle_other_deg 1.361 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10816 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 116
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction