7YAO | pdb_00007yao

Crystal structure of a bright green fluorescent protein (oxStayGold) 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		AF2 predicted

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.1M DL-Malic acid pH7.0

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.107	α = 90
b = 132.107	β = 90
c = 58.887	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		2022-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.18058	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	1.5	43.96	100	0.072	20.6	9.9		93826

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	1.5	1.53			0.888

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	1.5	43.96	93790	4630	99.991	0.161	0.1598	0.17	0.1777	0.18	15.989

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]
0.171	0.085		0.171		-0.553

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.135
r_dihedral_angle_4_deg	14.771
r_dihedral_angle_3_deg	12.024
r_dihedral_angle_1_deg	7.449
r_lrange_it	5.33
r_lrange_other	4.875
r_scangle_it	2.855
r_scangle_other	2.855
r_scbond_it	1.821
r_scbond_other	1.82
r_angle_refined_deg	1.587
r_mcangle_it	1.567
r_mcangle_other	1.566
r_angle_other_deg	1.408
r_mcbond_it	0.966
r_mcbond_other	0.966
r_symmetry_nbd_refined	0.292
r_nbd_other	0.256
r_nbd_refined	0.255
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3438
Nucleic Acid Atoms
Solvent Atoms	705
Heterogen Atoms	38

Software

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