3HZ4 | pdb_00003hz4

Crystal Structure of Thioredoxin from Methanosarcina mazei

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	20% Peg 3350, 0.1M Bis Tris pH 5.5, 0.2M LiSo4, 0.1M EDTA, 20% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.068	α = 90
b = 82.068	β = 90
c = 93.874	γ = 120

Symmetry
Space Group	P 32 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 315r	Mirrors	2009-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9797	NSLS	X29A

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	2.3	50	94.8	0.13	0.13	9.9	21.5	18041	18041

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)
	2.3	2.38	100		0.39	9.6	21	1639

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	50	18040	17112	927	94.83	0.19335	0.19053	0.1873	0.24659	0.2369	RANDOM	23.48

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]
0.81	0.4		0.81		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.382
r_dihedral_angle_3_deg	21.371
r_dihedral_angle_4_deg	18.226
r_dihedral_angle_1_deg	7.426
r_scangle_it	5.763
r_scbond_it	3.812
r_mcangle_it	2.215
r_angle_refined_deg	2.086
r_mcbond_it	1.659
r_symmetry_hbond_refined	0.429
r_nbtor_refined	0.325
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.201
r_chiral_restr	0.193
r_xyhbond_nbd_refined	0.175
r_bond_refined_d	0.025
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1932
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing