6UWE | pdb_00006uwe

Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio paradoxus saturated with copper

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10 mg/mL TcDH in 25 mM borate buffer, pH 9.5 was mixed with 0.17 M ammonium acetate, 0.085 M sodium citrate, pH 5.6, 25.5% w/v PEG 4000, 15% glycerol. To increase copper incorporation, powder of CuCl was added to drops with crystals 30-40 min prior to harvesting. Sodium cyanate solution was added to the drop with crystals to the final concertation of ~100 mM at the same time as CuCl was added.

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.422	α = 90
b = 163.149	β = 119.29
c = 90.631	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	PIXEL	DECTRIS PILATUS 6M		2017-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.96900	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.6	50	94.4	0.074	0.074	0.092	0.053	0.993	9.3	2.6		285581		-3	15.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	92.6		0.461	0.461	0.575	0.341	0.692	2.1	2.6

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6I3Q	1.6	44.8	261930	13391	90.98	0.1424	0.1415	0.1602	RANDOM	15.065

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]
-0.32		0.38	1.41		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.656
r_dihedral_angle_1_deg	20.132
r_dihedral_angle_4_deg	20.011
r_dihedral_angle_3_deg	12.342
r_angle_refined_deg	1.511
r_angle_other_deg	1.38
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.656
r_dihedral_angle_1_deg	20.132
r_dihedral_angle_4_deg	20.011
r_dihedral_angle_3_deg	12.342
r_angle_refined_deg	1.511
r_angle_other_deg	1.38
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14560
Nucleic Acid Atoms
Solvent Atoms	2369
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
Coot	refinement

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.