1R26 | pdb_00001r26

Crystal structure of thioredoxin from Trypanosoma brucei brucei

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	2M sodium formate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.878	α = 90
b = 51.725	β = 90
c = 57.389	γ = 90

Symmetry
Space Group	P 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 4		2001-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9150	ESRF	ID29

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	1.4	30	99.6	0.078	0.078	5.8	10	22807	22807

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	1.4	1.45	100		0.515	0.01	1	10.4	23274

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Pdb entry 1ert polyala	1.4	30	21601	21601	1165	99.68	0.16827	0.1691	0.16762	0.17	0.19841	RANDOM	14.589

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]
0.57			-0.36		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.511
r_scangle_it	4.229
r_scbond_it	2.478
r_mcangle_it	1.67
r_angle_refined_deg	1.327
r_mcbond_it	0.88
r_angle_other_deg	0.763
r_nbd_refined	0.283
r_symmetry_vdw_other	0.26
r_nbd_other	0.25
r_xyhbond_nbd_refined	0.187
r_symmetry_vdw_refined	0.168
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.083
r_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	904
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
AMoRE	phasing
REFMAC	refinement