8J2J | pdb_00008j2j

Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (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 sulfate,0.1 M BisTris pH5.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.58	α = 90
b = 134.58	β = 90
c = 58.449	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	1.9	19.73	99.9	0.121	8.9	4.1		47721

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	1.9	1.94			0.626

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	1.9	19.73	47709	2364	99.82	0.162	0.1599	0.17	0.2055	0.21	20.252

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]
0.459	0.229		0.459		-1.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.891
r_dihedral_angle_3_deg	12.619
r_dihedral_angle_4_deg	11.693
r_dihedral_angle_1_deg	7.647
r_lrange_it	6.07
r_lrange_other	5.736
r_scangle_it	3.608
r_scangle_other	3.584
r_scbond_it	2.217
r_scbond_other	2.198
r_mcangle_it	2.154
r_mcangle_other	2.154
r_angle_refined_deg	1.567
r_mcbond_it	1.356
r_mcbond_other	1.354
r_angle_other_deg	1.283
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.2
r_symmetry_nbd_other	0.181
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3424
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	47

Software

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