3M9K | pdb_00003m9k

Crystal structure of human thioredoxin C69/73S double-mutant, oxidized form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	298	1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.62	α = 90
b = 125.62	β = 90
c = 33.55	γ = 120

Symmetry
Space Group	P 6

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 325 mm CCD	RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR	2009-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

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	1.5	22.43	98.6	0.053	15.2	9.89		48316			29.9

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)
	1.5	1.55	97.8		0.631	2.8	9.16

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ERT	1.5	22.34	48316	2445	98.6	0.185	0.184	0.19	0.211	0.22	RANDOM	23.87

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]
0.22	0.11		0.22		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_dihedral_angle_3_deg	14.519
r_sphericity_free	9.192
r_scangle_it	5.54
r_dihedral_angle_1_deg	5.513
r_scbond_it	3.724
r_sphericity_bonded	3.531
r_mcangle_it	2.547
r_rigid_bond_restr	1.807
r_angle_refined_deg	1.731
r_mcbond_it	1.664
r_angle_other_deg	0.95
r_mcbond_other	0.763
r_chiral_restr	0.104
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1642
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing