3GB5 | pdb_00003gb5

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	20% PEG 3000, 0.1 M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.756	α = 90
b = 87.756	β = 90
c = 62.652	γ = 120

Symmetry
Space Group	P 31 2 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 315r		2008-04-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.653	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.8			36382	36382

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	99		4.3	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2	50	19113	19113	984	99.8	0.169	0.169	0.167	0.1638	0.189	0.1838	RANDOM	32.568

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]
0.38	0.19		0.38		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.485
r_dihedral_angle_1_deg	16.679
r_dihedral_angle_3_deg	14.079
r_dihedral_angle_4_deg	11.962
r_scangle_it	4.326
r_scbond_it	2.803
r_mcangle_it	1.606
r_angle_refined_deg	1.569
r_mcbond_it	1.121
r_nbtor_refined	0.298
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.121
r_symmetry_hbond_refined	0.105
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1479
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing