6J1B | pdb_00006j1b

Photoswitchable fluorescent protein Gamillus, N150C/T204V double mutant, on-state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	mmonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.0

Crystal Properties
Matthews coefficient	Solvent content
5.77	78.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.492	α = 90
b = 161.492	β = 90
c = 161.492	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2018-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.99	46.619	100	0.071	0.073	0.999	27.64	14.402		47626			26.014

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	1.99	2.12	100		0.254	0.264	0.986	8.75	13.78

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5Y00	1.99	46.62	45244	2382	99.99	0.1435	0.1427	0.16	0.1602	0.17	RANDOM	22.005

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
r_dihedral_angle_2_deg	36.156
r_dihedral_angle_4_deg	14.563
r_dihedral_angle_3_deg	12.136
r_dihedral_angle_1_deg	7.196
r_angle_refined_deg	2.709
r_angle_other_deg	1.214
r_chiral_restr	0.169
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.156
r_dihedral_angle_4_deg	14.563
r_dihedral_angle_3_deg	12.136
r_dihedral_angle_1_deg	7.196
r_angle_refined_deg	2.709
r_angle_other_deg	1.214
r_chiral_restr	0.169
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1811
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	483

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.