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Crystal structure of a bright green fluorescent protein (oxStayGold) in jellyfish Cytaeis uchidae from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF2 predicted
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.1M DL-Malic acid pH7.0
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.107 α = 90 b = 132.107 β = 90 c = 58.887 γ = 120
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 PILATUS3 6M 2022-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18058 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 43.96 100 0.072 20.6 9.9 93826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.888
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF2 predicted 1.5 43.96 93790 4630 99.991 0.161 0.1598 0.1665 0.1777 0.1831 15.989
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] 0.171 0.085 0.171 -0.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.135 r_dihedral_angle_4_deg 14.771 r_dihedral_angle_3_deg 12.024 r_dihedral_angle_1_deg 7.449 r_lrange_it 5.33 r_lrange_other 4.875 r_scangle_it 2.855 r_scangle_other 2.855 r_scbond_it 1.821 r_scbond_other 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.135 r_dihedral_angle_4_deg 14.771 r_dihedral_angle_3_deg 12.024 r_dihedral_angle_1_deg 7.449 r_lrange_it 5.33 r_lrange_other 4.875 r_scangle_it 2.855 r_scangle_other 2.855 r_scbond_it 1.821 r_scbond_other 1.82 r_angle_refined_deg 1.587 r_mcangle_it 1.567 r_mcangle_other 1.566 r_angle_other_deg 1.408 r_mcbond_it 0.966 r_mcbond_other 0.966 r_symmetry_nbd_refined 0.292 r_nbd_other 0.256 r_nbd_refined 0.255 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3438 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing