3EMX | pdb_00003emx

Crystal structure of thioredoxin from Aeropyrum pernix

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	100mM Hepes pH 7.5, 1.4M sodium tri-citrate, Vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.229	α = 90
b = 54.852	β = 90
c = 159.342	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 225 mm CCD		2008-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97958	CLSI	08ID-1

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	2.25	30.817	99.8	0.109	0.109	16.5	9.2	11259	11236			26.7

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)
	2.25	2.37	99.9		0.45	0.45	3.8	5	1629

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.25	20	11226	11217	552	99.92	0.198	0.195	0.254	0.2046	RANDOM	25.857

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]
-0.82			-0.18		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.748
r_dihedral_angle_4_deg	19.879
r_dihedral_angle_3_deg	17.783
r_dihedral_angle_1_deg	5.726
r_scangle_it	3.362
r_scbond_it	1.939
r_angle_refined_deg	1.321
r_mcangle_it	1.139
r_mcbond_it	0.573
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1948
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SHELXCD	phasing
SHELXE	model building