3GH8 | pdb_00003gh8

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and di-iodotyrosine (DIT)

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	5.5	293	0.2M Ammonium acetate, 45% 2-Methyl-2,4-pentanediol, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.61	α = 90
b = 112.567	β = 89.92
c = 189.253	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 315r		2008-04-04		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	2.6	50	97.1	0.086	0.086	9.7	2.6	62935	62878		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	92.9		0.295	2.4	2.5	5984

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2.61	30	62878	3202	96.82	0.185	0.185	0.181	0.18	0.264	0.26	RANDOM	35.532

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]
-1.13		-0.16	-4.05		5.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.104
r_dihedral_angle_3_deg	20.523
r_dihedral_angle_4_deg	19.877
r_dihedral_angle_1_deg	7.36
r_scangle_it	3.693
r_scbond_it	2.338
r_angle_refined_deg	1.926
r_mcangle_it	1.502
r_mcbond_it	0.832
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.104
r_dihedral_angle_3_deg	20.523
r_dihedral_angle_4_deg	19.877
r_dihedral_angle_1_deg	7.36
r_scangle_it	3.693
r_scbond_it	2.338
r_angle_refined_deg	1.926
r_mcangle_it	1.502
r_mcbond_it	0.832
r_nbtor_refined	0.324
r_nbd_refined	0.251
r_symmetry_vdw_refined	0.206
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.137
r_symmetry_hbond_refined	0.11
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14232
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	378

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.