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Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (N137A) in jellyfish Cytaeis uchidae from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M Sodium citrate tribasic dihydrate pH6.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.207 α = 90 b = 134.207 β = 90 c = 58.628 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 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.7 19.72 99.9 0.12 15.8 11 66343
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 1.061
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 AlphaFold 1.7 19.72 66313 3478 99.923 0.146 0.145 0.1579 0.1703 0.1809 18.612
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] 0.399 0.199 0.399 -1.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 13.417 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 7.11 r_lrange_it 7.108 r_lrange_other 6.947 r_scangle_it 5.354 r_scangle_other 5.353 r_scbond_it 3.41 r_scbond_other 3.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 13.417 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 7.11 r_lrange_it 7.108 r_lrange_other 6.947 r_scangle_it 5.354 r_scangle_other 5.353 r_scbond_it 3.41 r_scbond_other 3.409 r_mcangle_other 2.682 r_mcangle_it 2.68 r_angle_refined_deg 1.828 r_mcbond_it 1.737 r_mcbond_other 1.732 r_angle_other_deg 1.441 r_symmetry_nbd_refined 0.372 r_nbd_other 0.244 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.212 r_symmetry_nbd_other 0.188 r_metal_ion_refined 0.186 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3420 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing