6SJI | pdb_00006sji

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OEX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	0.17M Ammonium acetate, 0.085 M Sodium cacjdilate pH 6.5, 25.5 % v/v Polyatilen glycol 8000, 15% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.08	α = 90
b = 160.41	β = 98.114
c = 90.88	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		2017-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.968623	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.8	90	96.2	0.122	0.987	6.63	2.7		176251

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	98		0.456	0.824	2.2	2.57

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OEX	1.8	89.97	176251	8761	96.253	0.161	0.1591	0.16	0.1984	0.2	23.99

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]
0.112		-1.128	0.176		0.032

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.672
r_dihedral_angle_4_deg	20.739
r_sphericity_bonded	16.629
r_dihedral_angle_3_deg	13.884
r_dihedral_angle_1_deg	7.447
r_lrange_it	5.394
r_scangle_it	4.336
r_scbond_it	3.011
r_mcangle_it	2.538
r_angle_refined_deg	1.937
r_mcbond_it	1.897
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.197
r_chiral_restr	0.145
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14585
Nucleic Acid Atoms
Solvent Atoms	1183
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing