1QY9

Crystal structure of E. coli Se-MET protein YDDE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	12% MPEG 5000, 0.2 M SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.035	α = 90
b = 56.529	β = 101.67
c = 148.742	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-03-11	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.05	20	99.7	0.066	7.3	3.9		80627

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.1	100		0.364	1.7	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	20	80286	1630	99.68	0.17203	0.17129	0.20672	RANDOM	23.184

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]
0.56		0.24	-0.9		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.188
r_scangle_it	3.394
r_scbond_it	2.031
r_mcangle_it	1.382
r_angle_refined_deg	1.2
r_angle_other_deg	0.762
r_mcbond_it	0.718
r_symmetry_vdw_other	0.256
r_nbd_other	0.242
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.126
r_symmetry_hbond_refined	0.107
r_nbtor_other	0.081
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9063
Nucleic Acid Atoms
Solvent Atoms	620
Heterogen Atoms	19

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing