4JGE

Crystal structure of red fluorescent gene-engineered variant with improved folding - lanRFP_delS83 (Branchiostoma lanceolatum)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JF9	PDB ENTRY 4JF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	35.6 mg/ml of lanRFP- S83 in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 0.2M Na2HPO4 0.1M Tris pH 7.0 20% PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.762	α = 90
b = 133.762	β = 90
c = 156.956	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.94	30	97.2	0.109	7.9	4		60055

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	1.94	2.01	89.1		0.425		3.9	5388

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4JF9	1.94	22.76	59838	1211	96.98	0.1566	0.1557	0.1982	RANDOM	20.5401

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	37.573
r_dihedral_angle_4_deg	22.337
r_dihedral_angle_3_deg	14.048
r_dihedral_angle_1_deg	7.039
r_scangle_it	5.892
r_scbond_it	3.869
r_mcangle_it	2.491
r_angle_refined_deg	2.332
r_mcbond_it	1.504
r_chiral_restr	0.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.573
r_dihedral_angle_4_deg	22.337
r_dihedral_angle_3_deg	14.048
r_dihedral_angle_1_deg	7.039
r_scangle_it	5.892
r_scbond_it	3.869
r_mcangle_it	2.491
r_angle_refined_deg	2.332
r_mcbond_it	1.504
r_chiral_restr	0.237
r_bond_refined_d	0.033
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3479
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.