2I4A | pdb_00002i4a

Crystal structure of thioredoxin from the acidophile Acetobacter aceti

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	microseeding in 100 mM sodium acetate (pH 4.6), 100 mM ammonium acetate, 24% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.94	α = 90
b = 42.24	β = 90
c = 63.67	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	CCD	NOIR-1		2006-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.07	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1	42.24	96.2	0.048	23.9	6.13		48392			7.9

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	1.04	67.9		0.479	1.8	2.8	3351

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 2trx	1	35.2	45895	2428	96.22	0.13465	0.13465	0.13346	0.14	0.1582	0.16	RANDOM	12.51

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]
-0.14			0.17		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.081
r_dihedral_angle_4_deg	28.105
r_sphericity_free	15.363
r_dihedral_angle_3_deg	11.38
r_scangle_it	6.804
r_dihedral_angle_1_deg	5.745
r_sphericity_bonded	5.443
r_scbond_it	4.973
r_mcangle_it	3.374
r_mcbond_it	2.711
r_rigid_bond_restr	2.307
r_angle_refined_deg	2.192
r_angle_other_deg	1.007
r_mcbond_other	0.965
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.223
r_symmetry_vdw_other	0.21
r_nbd_other	0.195
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.146
r_nbtor_other	0.098
r_bond_refined_d	0.034
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1684
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
JBluIce-EPICS	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing