9YUV | pdb_00009yuv

Crystal structure of sulfoquinovose dioxygenase from Marinobacterium aestuarii in complex with Mn(II) and alpha-ketoglutarate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.697	α = 90
b = 117.68	β = 90
c = 59.359	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER X 16M		2024-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.035	47.683	99.8	1	11.2	6.7		24768

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.09			0.61

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	2.035	47.683	24754	1303	99.73	0.193	0.1913	0.1998	0.2277	0.2313	41.329

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]
1.041			0.798		-1.839

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.638
r_dihedral_angle_6_deg	14.213
r_lrange_it	7.623
r_lrange_other	7.602
r_dihedral_angle_2_deg	7.484
r_dihedral_angle_1_deg	6.702
r_scangle_it	6.046
r_scangle_other	6.029
r_scbond_it	3.895
r_scbond_other	3.874
r_mcangle_it	3.87
r_mcangle_other	3.869
r_mcbond_it	2.669
r_mcbond_other	2.668
r_angle_refined_deg	1.374
r_angle_other_deg	0.49
r_nbd_refined	0.195
r_nbd_other	0.192
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.173
r_symmetry_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.069
r_metal_ion_refined	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2529
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing