3GFD | pdb_00003gfd

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GB5	PDB entry 3GB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	20% PEG 3350, 0.2M MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.32	71.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.187	α = 90
b = 105.187	β = 90
c = 162.124	γ = 120

Symmetry
Space Group	P 32 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		2008-06-08		SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.45	50	99.2	0.081	0.081	20	4.7	38478	38170		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.54	99.3		0.439	0.439	3.7	4.7	3783

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3GB5	2.45	30	36506	36214	1925	99.2	0.145	0.145	0.144	0.14	0.178	0.18	RANDOM	38.779

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]
1.88	0.94		1.88		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.159
r_dihedral_angle_4_deg	19.385
r_dihedral_angle_1_deg	17.323
r_dihedral_angle_3_deg	16.196
r_scangle_it	5.026
r_scbond_it	3.002
r_angle_refined_deg	2.016
r_mcangle_it	1.736
r_mcbond_it	0.947
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.159
r_dihedral_angle_4_deg	19.385
r_dihedral_angle_1_deg	17.323
r_dihedral_angle_3_deg	16.196
r_scangle_it	5.026
r_scbond_it	3.002
r_angle_refined_deg	2.016
r_mcangle_it	1.736
r_mcbond_it	0.947
r_nbtor_refined	0.32
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.181
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.141
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3550
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	108

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.