2IFQ | pdb_00002ifq

Crystal structure of S-nitroso thioredoxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HXK	PDB entry 2HXK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.08	α = 90
b = 25.749	β = 97.97
c = 85.86	γ = 90

Symmetry
Space Group	C 1 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 315	bent Si-mirror	2006-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-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	1.2	25.1	97.1	0.07	9.1	5.1	79717	79717			16.5

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	1.24	98.4		0.24	3.3	4.8	7774

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2HXK	1.2	25.13	73521	73521	3882	97.1	0.17859	0.17716	0.19	0.20565	0.21	RANDOM	13.78

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]
-0.39		-0.03	0.25		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.516
r_dihedral_angle_3_deg	14.112
r_sphericity_free	11.053
r_dihedral_angle_1_deg	6.275
r_sphericity_bonded	5.508
r_scangle_it	5.499
r_scbond_it	4.278
r_mcangle_it	3.07
r_rigid_bond_restr	2.655
r_mcbond_it	2.548
r_angle_refined_deg	1.96
r_mcbond_other	1.374
r_angle_other_deg	0.998
r_symmetry_vdw_refined	0.335
r_nbd_refined	0.276
r_symmetry_vdw_other	0.249
r_nbd_other	0.192
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.13
r_nbtor_other	0.109
r_chiral_restr	0.103
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2685
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data collection
CrystalClear	data reduction
CrystalClear	data scaling