9YUT | pdb_00009yut

Crystal structure of malonate-bound sulfoquinovose dioxygenase from Marinobacterium aestuarii

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	1.8 - 2.1 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.041	α = 90
b = 117.117	β = 90
c = 59.323	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		2024-03-07	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	1.42	47.66	99.7	1	12.3	6.7		71275

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	1.42	1.45			0.77

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	1.422	47.656	71255	3599	99.655	0.127	0.125	0.1249	0.1565	0.1565	16.571

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]
0.641			-0.12		-0.521

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.049
r_lrange_it	14.879
r_lrange_other	12.88
r_dihedral_angle_3_deg	11.635
r_dihedral_angle_2_deg	9.854
r_scangle_it	8.087
r_scangle_other	8.084
r_dihedral_angle_1_deg	6.315
r_mcangle_it	5.781
r_mcangle_other	5.78
r_scbond_it	5.392
r_scbond_other	5.382
r_mcbond_it	3.803
r_mcbond_other	3.798
r_rigid_bond_restr	2.869
r_angle_refined_deg	1.556
r_angle_other_deg	0.577
r_symmetry_nbd_refined	0.258
r_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.213
r_nbd_other	0.193
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.174
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2531
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	14

Software

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