4KEX | pdb_00004kex

Crystal structure analysis of a single amino acid deletion mutation in EGFP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4	291	0.1 M MMT Buffer (Malic acid, MES and Tris), 25% (w/v) PEG 1500, pH 4.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.45	α = 90
b = 63.14	β = 90
c = 65.7	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97630	Diamond	I04

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	1.6	51.45	98.1	0.092	15.2	7.9		28209			13.4

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	PDB ENTRY 4EUL	1.6	45.57	28165	1417	97.77	0.1837	0.1823	0.1914	0.2092	0.2159	RANDOM	17.9795

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]
-0.22			0.28		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.722
r_dihedral_angle_4_deg	15.534
r_dihedral_angle_3_deg	14.847
r_dihedral_angle_1_deg	6.942
r_angle_refined_deg	2.139
r_angle_other_deg	0.939
r_chiral_restr	0.139
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1804
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction