2EIQ | pdb_00002eiq

Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TRX	PDB ENTRY 2TRX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	277	40% MPD, 1MM CUPRIC ACETATE, 10MM SODIUM ACETATE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.209	α = 90
b = 49.557	β = 113.33
c = 59.427	γ = 90

Symmetry
Space Group	C 1 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 210	MIRROR	2005-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A		Photon Factory	AR-NW12A

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	54.55	99.5	0.083	0.083		3.7	18923	18812

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	1.9	1.97	99.9		0.304	0.304		3.7

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	PDB ENTRY 2TRX	1.9	41.6	16882	1930	99.47	0.18731	0.18374	0.1843	0.21845	0.2186	RANDOM	18.98

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]
-0.35		-0.29	1.05		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.951
r_dihedral_angle_3_deg	12.627
r_dihedral_angle_4_deg	11.566
r_dihedral_angle_1_deg	4.951
r_scangle_it	4.59
r_scbond_it	2.98
r_mcangle_it	1.884
r_angle_refined_deg	1.584
r_mcbond_it	1.233
r_symmetry_vdw_refined	0.394
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.275
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.111
r_metal_ion_refined	0.039
r_bond_refined_d	0.017
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_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	1627
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	refinement