3DML | pdb_00003dml

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	291	0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, 3% (w/v) glucose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.909	α = 90
b = 80.909	β = 90
c = 33.212	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	MARMOSAIC 225 mm CCD	mirrors	2006-09-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.95369, 0.97833, 0.97838, 1.0332	EMBL/DESY, HAMBURG	X12

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	1.9	20.71	99.3	0.083	0.083	30.87	6.3	10064	9998			18.37

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)
	1.9	1.94	97.9		0.447	0.447	6.36	5.1	662

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	20.71	9557	9530	480	99.72	0.15668	0.15668	0.1544	0.1541	0.20124	0.2031	RANDOM	22.168

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]
0.3	0.15		0.3		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.723
r_dihedral_angle_4_deg	19.553
r_dihedral_angle_3_deg	15.954
r_dihedral_angle_1_deg	5.667
r_scangle_it	4.157
r_scbond_it	2.847
r_mcangle_it	1.738
r_mcbond_it	1.659
r_angle_refined_deg	1.512
r_nbtor_refined	0.32
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.216
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.098
r_bond_refined_d	0.012
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	799
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing