3DXB | pdb_00003dxb

Structure of the UHM domain of Puf60 fused to thioredoxin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TRX	8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8
experimental model	PDB	2PE8	8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.12	α = 90
b = 89.43	β = 90
c = 299.39	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	MARMOSAIC 225 mm CCD	LN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror Beamline suitable for large unit cell structures	2007-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.006	SLS	X06SA

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	2.2	49.832	99.8	0.11	0.106	14.53	6.1	103128	102916	1	1	36.481

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	2.2	2.33	98.9		0.393	0.604	3.24	5.8	16266

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8	2.2	49.75	2	103128	102916	5181	99.8	0.21419	0.21419	0.2112	0.23	0.27148	0.28	RANDOM	21.623

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]
1.99			-1.26		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.874
r_dihedral_angle_4_deg	17.097
r_dihedral_angle_3_deg	15.816
r_dihedral_angle_1_deg	5.682
r_angle_refined_deg	1.012
r_scangle_it	0.921
r_scbond_it	0.597
r_mcangle_it	0.432
r_mcbond_it	0.341
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.874
r_dihedral_angle_4_deg	17.097
r_dihedral_angle_3_deg	15.816
r_dihedral_angle_1_deg	5.682
r_angle_refined_deg	1.012
r_scangle_it	0.921
r_scbond_it	0.597
r_mcangle_it	0.432
r_mcbond_it	0.341
r_nbtor_refined	0.298
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13074
Nucleic Acid Atoms
Solvent Atoms	1191
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.