3D4T

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (oxidized form)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	291	0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81	α = 90
b = 81	β = 90
c = 33.1	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	OXFORD ONYX CCD	mirrors	2006-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OXFORD DIFFRACTION ENHANCED ULTRA

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	2.05	12.04	99.52	0.125	0.125	36.02	33.61	8063	7981			17.26

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)
	2.05	2.16	100		0.5	0.5	6.15	19.65	1152

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	derived from SoxS MAD data	2.05	12.04	7621	389	100	0.17681	0.17681	0.17476	0.21637	RANDOM	16.424

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.787
r_dihedral_angle_1_deg	19.516
r_dihedral_angle_4_deg	16.317
r_dihedral_angle_3_deg	15.425
r_scangle_it	3.264
r_scbond_it	2.048
r_angle_refined_deg	1.608
r_mcangle_it	1.497
r_mcbond_it	0.914
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.196
r_chiral_restr	0.155
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	789
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing