8S5B | pdb_00008s5b

Crystal structure of the sulfoquinovosyl binding protein (SmoF) from A. tumefaciens sulfo-SMO pathway in complex with SQOctyl ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OFY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	200 mM calcium acetate, 100 mM Bis-TRIS pH 6.5, 25% w/v PEG 2000 MME, 1:1 protein:mother liquor ratio with SmoF at 50mg/ml in 50mM TRIS, 300mM NaCl pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.777	α = 90
b = 65.851	β = 90
c = 107.018	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS 6M-F		2019-02-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.8	56.147	100	0.116	0.134	0.065	0.965	10.1	8		36036

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	1.8	1.84			0.47	0.54	0.262	0.952		7.9

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	1.8	56.147	35966	1842	99.939	0.228	0.2255	0.23	0.2716	0.28	19.01

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]
-3.167			-0.187		3.355

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.487
r_dihedral_angle_4_deg	16.493
r_dihedral_angle_3_deg	13.497
r_dihedral_angle_1_deg	6.136
r_lrange_it	3.792
r_lrange_other	3.735
r_scangle_it	2.614
r_scangle_other	2.613
r_mcangle_it	1.976
r_mcangle_other	1.976
r_scbond_it	1.744
r_scbond_other	1.744
r_angle_refined_deg	1.552
r_mcbond_it	1.385
r_angle_other_deg	1.384
r_mcbond_other	1.376
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.174
r_nbd_other	0.171
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2838
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing