8S5S | pdb_00008s5s

Crystal structure of a Sulfite dehydrogenase from Thermus thermophilus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y0K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	14% PEG 8000, 0.1 M sodium citrate tribasic dihydrate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.02	α = 90
b = 130.02	β = 90
c = 114.79	γ = 120

Symmetry
Space Group	P 61 2 2

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 PILATUS3 6M		2019-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96851	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.85	42.56	99.94	0.02516	0.999	16.83	12.2		49202			31.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.916	99.96		0.3857	0.733	2.46	12.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.85	42.559	49202	2000	99.961	0.166	0.1653	0.1765	0.192	0.1992	33.1

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]
-0.295	-0.147		-0.295		0.956

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.567
r_dihedral_angle_3_deg	12.848
r_dihedral_angle_2_deg	9.001
r_lrange_it	8.608
r_lrange_other	8.592
r_scangle_it	7.346
r_scangle_other	7.345
r_dihedral_angle_1_deg	6.647
r_scbond_it	4.921
r_scbond_other	4.919
r_mcangle_other	3.85
r_mcangle_it	3.84
r_mcbond_it	3.022
r_mcbond_other	3.021
r_angle_refined_deg	1.926
r_angle_other_deg	0.617
r_nbd_refined	0.215
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.162
r_nbd_other	0.136
r_symmetry_xyhbond_nbd_refined	0.098
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.087
r_symmetry_nbd_refined	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_dihedral_angle_other_3_deg	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2974
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	27

Software

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