1YFG | pdb_00001yfg

YEAST INITIATOR TRNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Schevitz et al (1979), 278, 188-190. (4A structure)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	301	pH 6.00, VAPOR DIFFUSION, temperature 301.00K

Crystal Properties
Matthews coefficient	Solvent content
5.16	82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.72	α = 90
b = 113.72	β = 90
c = 136.541	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	278	FILM			1988-01-01	M
2	1	x-ray	278	STORAGE PHOSPHORS	KODAK		1988-01-01	M
3	1	x-ray	278	IMAGE PLATE	Y.AMEMIYA		1988-01-01	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL		SSRL
2	SYNCHROTRON	CHESS		CHESS
3	SYNCHROTRON	PHOTON FACTORY		Photon Factory

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2,3	3	20	95	0.08	15.7			10688

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	3	3.14	98.8		0.495	2.24

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MIR	NONE	4 A STRUCTURE REPORTED IN REFERENCE 2	3	10	1		81.7	0.215			33

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
p_chiral_restr	0.247
p_multtor_nbd	0.168
p_singtor_nbd	0.115
p_angle_d	0.025
p_bond_d	0.012
p_plane_restr	0.002
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1639
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHARE	model building
DENMOD	model building
NUCLIN/PROFFT	refinement
MODIFIED	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
NUCLIN	refinement
PROFFT	refinement