Experiment: 8ZUQ

Crystal structure of the F99S/M153T/V163A/T203I/E222Q variant of GFP at pH 8.5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JGJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		308	PEG 4000, magnesium chloride, MES-NaOH buffer (pH 5.0)

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.498	α = 90
b = 62.452	β = 90
c = 67.783	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	15	PIXEL	DECTRIS EIGER X 16M		2022-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.70	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.48	45.93	100	0.16	0.174	0.994	7.34	6.7		36411			11.51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.57	100		0.784	0.847	0.807	1.98	6.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.48	45.93	1.36	36405	1819	99.96	0.1578	0.156	0.1561	0.1931	0.1939	17.08

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.9406
f_angle_d	0.8351
f_chiral_restr	0.0836
f_plane_restr	0.0071
f_bond_d	0.0054

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1819
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing