Experiment: 5D08

Crystal structure of selenomethionine-labeled epoxyqueuosine reductase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	294	0.1 M acetate (pH 4.5), 0.4 M (NH4)H2PO4, 12% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.301	α = 90
b = 95.78	β = 90
c = 111.175	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	100	PIXEL	DECTRIS PILATUS 6M		2013-02-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9795, 0.9793, 0.9421	APS	24-ID-C

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	1.747	50	94.8	0.084	6.3	4.7		86822			18.35

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	1.75	1.81	93		0.578		4.3	8402

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	FREE R-VALUE	1.747	46.407	1.35	86579	4338	94.48	0.1688	0.1673	0.1705	0.1958	0.1981	Random selection	28.0559

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
f_dihedral_angle_d	13.003
f_angle_d	0.954
f_chiral_restr	0.039
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5962
Nucleic Acid Atoms
Solvent Atoms	638
Heterogen Atoms	238

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction