4KND | pdb_00004knd

Thioredoxin from Anaeromyxobacter dehalogenans.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.2 M sodium chloride, 0.1 M Tris-Cl buffer, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.731	α = 90
b = 76.954	β = 90
c = 77.208	γ = 90

Symmetry
Space Group	I 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	ADSC QUANTUM 315r		2013-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	38.51	98.4	0.086	11.7	7.1	15171	15171			52.3

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)
1	1.9	1.93	96.7		0.631	2.03	6.1	723

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	38.51	15170	15170	754	98.11	0.1846	0.1846	0.1828	0.2169	0.2475	RANDOM	52.864

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]
-0.41			4.55		-4.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.193
r_dihedral_angle_4_deg	20.387
r_dihedral_angle_3_deg	15.54
r_dihedral_angle_1_deg	6.246
r_angle_refined_deg	1.767
r_angle_other_deg	0.827
r_chiral_restr	0.093
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1611
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing