4J88 | pdb_00004j88

Dark-state structure of sfGFP containing the unnatural amino acid p-azido-phenylalanine at residue 66

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	278	10 mg/mL protein and 100 mM Tris-HCl, pH 8.3, 2.8 M (NH4)2SO4 (200+200 nanoL drop against 60 microL reservoir), VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.43	α = 90
b = 97.56	β = 90
c = 102.9	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	100	CCD	ADSC QUANTUM 315r	mirrors	2011-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.08	102.9	100	0.131	0.131	13.6	7.9	32505	32505			25.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.13	100		0.818	0.818	0.9	8.1	2360

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2B3P	2.08	48.78	32505	32445	1644	99.96	0.1654	0.1684	0.1654	0.17	0.2282	0.23	RANDOM	29.452

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]
2.09			-0.72		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.718
r_dihedral_angle_3_deg	15.87
r_dihedral_angle_4_deg	12.066
r_dihedral_angle_1_deg	7.862
r_angle_refined_deg	1.194
r_angle_other_deg	0.779
r_chiral_restr	0.033
r_bond_refined_d	0.021
r_bond_other_d	0.013
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.718
r_dihedral_angle_3_deg	15.87
r_dihedral_angle_4_deg	12.066
r_dihedral_angle_1_deg	7.862
r_angle_refined_deg	1.194
r_angle_other_deg	0.779
r_chiral_restr	0.033
r_bond_refined_d	0.021
r_bond_other_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3598
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	165

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
xia2	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.