9YUW | pdb_00009yuw

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

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
2.64	53.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.888	α = 90
b = 117.974	β = 90
c = 59.505	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	2.1	47.794	99.7	1	13.3	6.8		22708

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	2.1	2.16			0.79

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	2.1	47.794	22694	1130	99.522	0.195	0.193	0.2009	0.2262	0.2291	41.311

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]
-0.012			0.932		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.075
r_dihedral_angle_6_deg	14.195
r_dihedral_angle_2_deg	8.934
r_dihedral_angle_1_deg	6.65
r_lrange_it	6.197
r_lrange_other	6.194
r_scangle_it	4.957
r_scangle_other	4.951
r_mcangle_it	3.644
r_mcangle_other	3.643
r_scbond_it	3.288
r_scbond_other	3.285
r_mcbond_it	2.614
r_mcbond_other	2.614
r_angle_refined_deg	1.355
r_angle_other_deg	0.475
r_symmetry_xyhbond_nbd_refined	0.205
r_nbd_refined	0.201
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.175
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.073
r_chiral_restr	0.064
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	2523
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	31

Software

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