7VEQ

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

X-RAY DIFFRACTION

---

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	8.5	293	2.0 M Ammonium dihydrogenphosphate 0.1 M Tris-HCl 2.0 mM Unsaturated trigalacturonic acid

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.855	α = 90
b = 151.663	β = 90
c = 179.52	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 4M		2020-10-24	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	1.696	48.217	97.8	0.086	11.1	5.02		76813

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	1.74			0.555	1.87

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	1.696	48.217	76813	3841	99.491	0.169	0.1677	0.195	19.515

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]
-0.247			-0.819		1.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.05
r_dihedral_angle_3_deg	11.632
r_dihedral_angle_4_deg	11.052
r_dihedral_angle_1_deg	6.267
r_lrange_it	5.985
r_lrange_other	5.954
r_scangle_it	5.572
r_scangle_other	5.571
r_scbond_it	4.322
r_scbond_other	4.321
r_mcangle_other	3.411
r_mcangle_it	3.399
r_mcbond_it	2.805
r_mcbond_other	2.785
r_angle_other_deg	2.224
r_angle_refined_deg	1.707
r_nbd_other	0.281
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_refined	0.225
r_symmetry_nbd_other	0.218
r_nbtor_refined	0.186
r_symmetry_nbd_refined	0.163
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.039
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	4846
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	6

Software

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