1YTN | pdb_00001ytn

HYDROLASE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	296	THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS BY THE HANGING DROP VAPOR DIFFUSION METHOD. DROP WAS COMPOSED OF EQUAL VOLUMES OF PROTEIN (23 MG/ML) AND RESERVOIR SOLUTION. RESERVOIR SOLUTION WAS 27% POLYETHYLENE GLYCOL (MW 1500), 10% 2-METHYL-2,4-PENTANEDIOL, 220 MM SODIUM NITRATE, 0.1% BETA-MERCAPTOETHANOL, AND 10 MM IMIDAZOLE, PH 7.2., vapor diffusion - hanging drop, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.09	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.7	α = 90
b = 49.7	β = 90
c = 99.5	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		AREA DETECTOR	XUONG-HAMLIN MULTIWIRE		1994-11-17	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

Data Collection

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	1YTW	2.4	7	9205		98	0.181	0.181		19

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]
5.098			9.347		-14.445

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	22.5
x_angle_deg	2.2
x_improper_angle_d	2.2
x_bond_d	0.02
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2173
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	4

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
PROCOR	data reduction
XSCALE	data scaling
X-PLOR	phasing