3GYK | pdb_00003gyk

The crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi DSS-3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.2M Lithium sulfate, 0.1M Tris-HCl, 2.0M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.836	α = 90
b = 91.7	β = 120
c = 67.911	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	SBC-3	mirror	2009-03-25	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97953	APS	19-BM

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	1.76	50	99.9	0.075	35	3.7	71433	71433

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	1.76	1.79	99.9		0.345	4.3	3.1	3518

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.76	50	67725	67725	3606	99.83	0.16194	0.16194	0.16006	0.1768	0.19753	0.2109	RANDOM	14.254

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]
-0.18			-0.42		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.648
r_dihedral_angle_4_deg	13.065
r_dihedral_angle_3_deg	12.547
r_dihedral_angle_1_deg	5.325
r_scangle_it	3.348
r_scbond_it	2.255
r_angle_refined_deg	1.344
r_mcangle_it	1.164
r_mcbond_it	0.671
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.648
r_dihedral_angle_4_deg	13.065
r_dihedral_angle_3_deg	12.547
r_dihedral_angle_1_deg	5.325
r_scangle_it	3.348
r_scbond_it	2.255
r_angle_refined_deg	1.344
r_mcangle_it	1.164
r_mcbond_it	0.671
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5323
Nucleic Acid Atoms
Solvent Atoms	752
Heterogen Atoms	99

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP/wARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.