8J2I | pdb_00008j2i

Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (Q140S) 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 NaCl, 0.1 M MES pH6.0, 20% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.154	α = 90
b = 135.154	β = 90
c = 58.508	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	1.75	19.78	99.9	0.101	20	14.8		61618

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	1.75	1.78			1.112

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	1.75	19.78	61591	3110	99.917	0.154	0.1523	0.16	0.184	0.19	23.273

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]
0.528	0.264		0.528		-1.712

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.648
r_dihedral_angle_3_deg	13.826
r_dihedral_angle_4_deg	12.722
r_dihedral_angle_1_deg	7.707
r_lrange_it	7.536
r_lrange_other	7.354
r_scangle_it	5.856
r_scangle_other	5.855
r_scbond_it	3.727
r_scbond_other	3.726
r_mcangle_it	2.925
r_mcangle_other	2.925
r_mcbond_it	2.049
r_mcbond_other	2.048
r_angle_refined_deg	1.816
r_angle_other_deg	1.426
r_symmetry_nbd_refined	0.351
r_nbd_other	0.316
r_symmetry_xyhbond_nbd_refined	0.284
r_nbd_refined	0.207
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3420
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	42

Software

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