7Y40

Crystal structure of a bright green fluorescent protein (StayGold) in jellyfish Cytaeis uchidae from Biortus

X-RAY DIFFRACTION

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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

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 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	R-Free	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	0.2054	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
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