7NBZ

Crystal structure of ligand free open conformation of sulfoquinovosyl binding protein (SQBP) from Agrobacterium tumefaciens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	279	0.3 M Ammonium Acetate 0.1 M Bis-TRIS pH 5.5 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2275825	44.81749

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.321	α = 109.039
b = 78.212	β = 106.865
c = 83.456	γ = 104.766

Symmetry
Space Group	P 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 EIGER X 16M		2018-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.35	72.014	93.3	0.995	11.1	2.1		234884

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	1.35	1.37			0.906

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	D_1292108223	1.35	72.014	234883	11842	93.253	0.184	0.1832	0.2095	14.291

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]
5.979	-2.035	1.372	-2.484	-0.188	-3.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.847
r_dihedral_angle_4_deg	17.957
r_dihedral_angle_3_deg	12.352
r_dihedral_angle_1_deg	5.625
r_lrange_it	4.149
r_lrange_other	4.149
r_scangle_it	3.122
r_scangle_other	3.122
r_angle_other_deg	2.373
r_scbond_it	2.156
r_scbond_other	2.156
r_mcangle_other	1.874
r_mcangle_it	1.873
r_angle_refined_deg	1.833
r_mcbond_it	1.32
r_mcbond_other	1.312
r_nbd_other	0.337
r_symmetry_nbd_refined	0.329
r_nbd_refined	0.225
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.132
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.071
r_bond_other_d	0.036
r_gen_planes_other	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8804
Nucleic Acid Atoms
Solvent Atoms	1464
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
autoPROC	data scaling
MOLREP	phasing