8J2K | pdb_00008j2k

Crystal structure of a bright green fluorescent protein (StayGold) with double mutation (N137A, 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 Lithium sulfate,0.1 M BisTris pH5.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.789	α = 90
b = 134.789	β = 90
c = 59.18	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	19.86	99.1	0.104	17.3	13.6		67008

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			0.968

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	19.86	66998	3428	99.129	0.154	0.1527	0.16	0.1831	0.19	21.445

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]
0.454	0.227		0.454		-1.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.513
r_dihedral_angle_4_deg	13.12
r_dihedral_angle_3_deg	12.524
r_dihedral_angle_1_deg	7.3
r_lrange_it	7.226
r_lrange_other	7.035
r_scangle_it	5.666
r_scangle_other	5.665
r_scbond_it	3.634
r_scbond_other	3.634
r_mcangle_other	2.564
r_mcangle_it	2.563
r_angle_refined_deg	1.85
r_mcbond_it	1.782
r_mcbond_other	1.779
r_angle_other_deg	1.429
r_symmetry_nbd_refined	0.299
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_other	0.235
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3406
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	42

Software

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