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Crystal structure of a bright green fluorescent protein (StayGold) 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 5.5 293 0.2 M Ammonium sulfate, 0.1 M BisTris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.975 α = 90 b = 134.975 β = 90 c = 59.041 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 S 6M 2022-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 44.44 100 0.089 24.5 20.4 67651
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 1.7 1.73 0.556
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 1.7 44.44 67621 3325 99.99 0.179 0.1778 0.1872 0.2054 0.2096 20.966
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] 0.627 0.313 0.627 -2.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_1_deg 21.895 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 12.668 r_lrange_it 5.063 r_lrange_other 4.812 r_scangle_it 2.825 r_scangle_other 2.825 r_mcangle_it 1.822 r_mcangle_other 1.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_1_deg 21.895 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 12.668 r_lrange_it 5.063 r_lrange_other 4.812 r_scangle_it 2.825 r_scangle_other 2.825 r_mcangle_it 1.822 r_mcangle_other 1.821 r_scbond_it 1.757 r_scbond_other 1.756 r_angle_refined_deg 1.504 r_angle_other_deg 1.257 r_mcbond_it 1.12 r_mcbond_other 1.12 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.179 r_nbd_refined 0.178 r_nbd_other 0.173 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3418 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing