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Crystal Structure of Cypridina Luciferase complexed with Oxyluciferin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 24NE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7 293 25mg/mL CLuc complexed with oxyluciferin, 3% polyethylene glycol monomethyl ether 2000, 7% polypropylene glycol 400, 2M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 4.61 73.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.648 α = 90 b = 144.648 β = 90 c = 186.154 γ = 120
Symmetry Space Group P 63 2 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 EIGER X 16M 2022-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980 Photon Factory BL-17A
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 3.14 47.35 99.8 0.221 0.233 0.071 0.999 14 19.5 20708
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 3.14 3.36 99.4 1.679 1.762 0.533 0.981 2.6 20.5
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 3.14 47.35 19624 1043 99.7 0.2685 0.26561 0.2655 0.32481 0.3141 RANDOM 124.53
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] 7.56 3.78 7.56 -24.52
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.492 r_long_range_B_other 25.492 r_scangle_other 20.682 r_mcangle_it 18.717 r_mcangle_other 18.714 r_scbond_it 14.492 r_scbond_other 14.491 r_dihedral_angle_3_deg 14.329 r_mcbond_it 12.811 r_mcbond_other 12.811
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.492 r_long_range_B_other 25.492 r_scangle_other 20.682 r_mcangle_it 18.717 r_mcangle_other 18.714 r_scbond_it 14.492 r_scbond_other 14.491 r_dihedral_angle_3_deg 14.329 r_mcbond_it 12.811 r_mcbond_other 12.811 r_dihedral_angle_1_deg 5.962 r_dihedral_angle_2_deg 5.347 r_angle_refined_deg 1.889 r_angle_other_deg 0.592 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4017 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing