8GYF | pdb_00008gyf

Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (K192Y) 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		293	0.2 M Ammonium formate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.707	α = 90
b = 134.707	β = 90
c = 58.568	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 EIGER X 9M		2022-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.946418	CLSI	08ID-1

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	2	44.235	98.8	0.261	7.9	9.3		40718

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	2	2.05			1.097	2.4

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	AF2 predicted	2	44.235	40712	1969	98.811	0.194	0.1916	0.2	0.2361	0.24	16.374

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	0.23		0.459		-1.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.214
r_dihedral_angle_4_deg	14.094
r_dihedral_angle_3_deg	13.095
r_dihedral_angle_1_deg	7.784
r_lrange_it	5.588
r_lrange_other	5.288
r_scangle_it	1.967
r_scangle_other	1.966
r_mcangle_it	1.716
r_mcangle_other	1.716
r_angle_refined_deg	1.529
r_angle_other_deg	1.22
r_scbond_it	1.177
r_scbond_other	1.176
r_mcbond_it	0.983
r_mcbond_other	0.983
r_nbd_refined	0.179
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_refined	0.173
r_nbd_other	0.169
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.097
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3424
Nucleic Acid Atoms
Solvent Atoms	625
Heterogen Atoms	46

Software

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