7VER

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in a full open conformation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25% PEG550MME 0.1 M MES 0.01 M Zinc sulfate 0.0209 mM Polygalacturonic acid sodium

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.961	α = 90
b = 84.727	β = 90
c = 90.025	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	100	PIXEL	DECTRIS EIGER X 4M		2021-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.699	48.848	98.3	0.045	33.3	10.7		66777

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8			0.253

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	7VEV	1.699	48.848	66774	3339	98.278	0.181	0.1797	0.2119	20.438

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]
0.419			-2.279		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.498
r_dihedral_angle_4_deg	13.253
r_dihedral_angle_3_deg	11.52
r_dihedral_angle_1_deg	6.122
r_lrange_it	4.771
r_lrange_other	4.721
r_scangle_it	4.58
r_scangle_other	4.579
r_scbond_it	3.655
r_scbond_other	3.654
r_mcangle_other	3.046
r_mcangle_it	3.036
r_mcbond_it	2.552
r_mcbond_other	2.533
r_angle_other_deg	2.223
r_angle_refined_deg	1.697
r_nbd_refined	0.223
r_symmetry_nbd_other	0.22
r_nbd_other	0.192
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.124
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.073
r_bond_other_d	0.034
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4851
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing