Experiment: 1YFP

STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EMA	PDB ENTRY 1EMA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	YFP WAS CONCENTRATED TO 10 MG/ML IN 50 MM HEPES PH 7.5. ROD-SHAPED CRYSTALS WITH APPROXIMATE DIMENSIONS OF 0.8 X 0.12 X 0.03 MM WERE GROWN IN HANGING DROPS CONTAINING 5 MICROLITERS PROTEIN AND 5 MICROLITERS MOTHER LIQUOR AT 15 DEGREES C AFTER 2 WEEKS. THE MOTHER LIQUOR CONTAINED 2.2 M SODIUM/POTASSIUM PHOSPHATE PH 6.9., vapor diffusion - hanging drop, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.308	α = 90
b = 117.655	β = 90
c = 62.919	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	RIGAKU	MIRRORS	1997-12-05	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.5	20	92	0.08	10.8	4		18916		1.9	28.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.56	94			4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1EMA	2.5	20	53039	18916		92	0.196	0.1791

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
t_dihedral_angle_d	20.36
t_it	4.4
t_angle_deg	1.72
t_trig_c_planes	0.09
t_nbd	0.04
t_bond_d	0.013
t_gen_planes	0.013
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1810
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

Software
Software Name	Purpose
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling
TNT	phasing