7YRE | pdb_00007yre

Crystal structure of a bright green fluorescent protein (StayGold) with triple mutations (N137A, Q140S, Y187F) 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	1 M Lithium chloride, 0.1 M Citrate pH4.0, 20% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.88	α = 90
b = 86.938	β = 109.66
c = 72.741	γ = 90

Symmetry
Space Group	P 1 21 1

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		2022-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.18062	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	2.3	48.13	98.9	0.038	12.3	3		35613

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	2.3	2.38			0.153

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	2.3	43.507	35594	1806	98.817	0.2	0.1968	0.2	0.253	0.25	31.791

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]
2.286		0.04	-1.892		-0.337

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.987
r_dihedral_angle_4_deg	15.653
r_dihedral_angle_3_deg	15.311
r_dihedral_angle_1_deg	8.09
r_lrange_it	5.526
r_lrange_other	5.465
r_scangle_it	3.697
r_scangle_other	3.697
r_mcangle_it	3.298
r_mcangle_other	3.297
r_scbond_it	2.275
r_scbond_other	2.275
r_mcbond_it	2.049
r_mcbond_other	2.048
r_angle_refined_deg	1.59
r_angle_other_deg	1.173
r_symmetry_nbd_refined	0.225
r_nbd_other	0.195
r_symmetry_nbd_other	0.184
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.049
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6692
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	80

Software

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