2FD3 | pdb_00002fd3

Crystal Structure of Thioredoxin Mutant P34H

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_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	8	277	60% (v/v) MPD, Hepes 15 mM, 1 mM Ac2Cu, pH 8.0, Counter-diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	38.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.138	α = 90
b = 90.041	β = 112.99
c = 36.326	γ = 90

Symmetry
Space Group	P 1 21 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	BRUKER SMART 6000	Montel Optics	2005-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.45	18.674	61.9	0.079	10.88	1.19	4223	4223			31.13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.45	2.5	47.8		0.3084	3.06	0.61	189

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_A	2.45	16.44	4013	193	62	0.18527	0.17983	0.18	0.30495	0.31	RANDOM	13.073

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]
-1.21		-0.4	0.56		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.803
r_dihedral_angle_3_deg	15.722
r_dihedral_angle_4_deg	13.315
r_dihedral_angle_1_deg	5.47
r_mcangle_it	1.399
r_angle_refined_deg	1.2
r_scangle_it	1.132
r_mcbond_it	0.867
r_scbond_it	0.742
r_nbtor_refined	0.291
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.003
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_refined
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	1685
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
SAINT	data scaling
SADABS	data scaling
XPREP	data reduction
MOLREP	phasing