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Crystal Structure of Cypridina luciferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7 293 25mg/mL CLuc, 3% polyethylene glycol monomethyl ether 2000, 7% polypropylene glycol 400, 2M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 4.56 73.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.37 α = 90 b = 144.37 β = 90 c = 186.71 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 4M 2022-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 2.70001 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.8 47.3 99.7 0.205 1 48.94 294 53534 59.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 98.8 2.878 0.983 2.73 152
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 SAD THROUGHOUT 3 47.3 22456 1198 99.91 0.23488 0.23307 0.2278 0.26841 0.256 RANDOM 100.966
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] 5.61 2.8 5.61 -18.19
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 17.439 r_long_range_B_refined 17.438 r_dihedral_angle_3_deg 13.315 r_scangle_other 12.737 r_mcangle_it 11.888 r_mcangle_other 11.885 r_scbond_it 8.991 r_scbond_other 8.989 r_mcbond_it 8.383 r_mcbond_other 8.379
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 17.439 r_long_range_B_refined 17.438 r_dihedral_angle_3_deg 13.315 r_scangle_other 12.737 r_mcangle_it 11.888 r_mcangle_other 11.885 r_scbond_it 8.991 r_scbond_other 8.989 r_mcbond_it 8.383 r_mcbond_other 8.379 r_dihedral_angle_1_deg 5.683 r_dihedral_angle_2_deg 3.516 r_angle_refined_deg 1.462 r_angle_other_deg 0.467 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 28
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction CRANK2 phasing