8J3J

Crystal structure of a bright green fluorescent protein (StayGold) with double mutations (Q140S, Y187F) in jellyfish Cytaeis uchidae from Biortus

X-RAY DIFFRACTION

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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	0.2 M Ammonium formate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.059	α = 90
b = 135.059	β = 90
c = 58.382	γ = 120

Symmetry
Space Group	P 61

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	19.77	99.9	0.095	13.5	7.8		66929

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			1.174

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold	1.7	19.77	66901	3414	99.925	0.169	0.1677	0.198	24.685

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]
0.573	0.286		0.573		-1.858

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_3_deg	13.806
r_dihedral_angle_4_deg	11.805
r_dihedral_angle_1_deg	7.744
r_lrange_it	7.257
r_lrange_other	7.064
r_scangle_it	5.537
r_scangle_other	5.536
r_scbond_it	3.492
r_scbond_other	3.491
r_mcangle_other	3.28
r_mcangle_it	3.278
r_mcbond_it	2.282
r_mcbond_other	2.272
r_angle_refined_deg	1.818
r_angle_other_deg	1.428
r_nbd_other	0.205
r_symmetry_xyhbond_nbd_refined	0.205
r_nbd_refined	0.195
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.145
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3418
Nucleic Acid Atoms
Solvent Atoms	556
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing