7OFX

Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	24% PEG 3350 w/v, 0.2 M KSCN, 0.1 M Bis-Tris propane pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.534	α = 90
b = 168.396	β = 116.53
c = 100.687	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 EIGER2 XE 16M		2019-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.15	61.51	97.4	0.09	0.109	0.061	0.993	8.1	2.9		153301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	98.9		0.686	0.829	0.459	0.624		2.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5OHT	2.15	61.01	145522	7734	97.36	0.1957	0.1942	0.2236	RANDOM	28.618

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]
0.58		-1.76	-0.38		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.461
r_dihedral_angle_4_deg	17.651
r_dihedral_angle_3_deg	13.885
r_dihedral_angle_1_deg	7.215
r_angle_refined_deg	1.502
r_angle_other_deg	1.347
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.461
r_dihedral_angle_4_deg	17.651
r_dihedral_angle_3_deg	13.885
r_dihedral_angle_1_deg	7.215
r_angle_refined_deg	1.502
r_angle_other_deg	1.347
r_chiral_restr	0.071
r_bond_refined_d	0.01
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	20405
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	80

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.