4J8A | pdb_00004j8a

Irradiated-state structure of sfGFP containing the unnatural amino acid p-azido-phenylalanine at residue 145

X-RAY DIFFRACTION

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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 M (NH4)2SO4, 200+200 nanoL drop against 60 microL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.5	α = 90
b = 58.7	β = 90
c = 91.63	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	PIXEL	PSI PILATUS 6M	Mirrors	2012-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.26	46.5	99.2	0.032	0.032	16	3.6	67853	67853			16.5

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	1.26	14.79	67742	67742	3429	98.92	0.1305	0.1305	0.1287	0.1271	0.1646	0.1627	RANDOM	23.5069

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]
1.58			-0.27		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.002
r_sphericity_bonded	16.785
r_dihedral_angle_4_deg	13.902
r_dihedral_angle_3_deg	12.863
r_rigid_bond_restr	8.851
r_dihedral_angle_1_deg	7.593
r_angle_refined_deg	1.586
r_angle_other_deg	0.672
r_chiral_restr	0.062
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	158

Software

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