7VEU

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with galacturonic acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	40% PEG600 0.1 M Citrate 50 mM Galacturonic acid sodium

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.686	α = 90
b = 86.662	β = 90
c = 97.323	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		2021-02-14	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	1.736	42.4	99.3	0.068	25.6	6.17		63700

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	1.74	1.84			0.529

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	1.736	40.436	63700	3185	99.257	0.157	0.1557	0.1812	18.611

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]
0.877			-1.128		0.251

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.914
r_dihedral_angle_4_deg	13.052
r_dihedral_angle_3_deg	12.777
r_dihedral_angle_1_deg	6.325
r_lrange_it	5.827
r_lrange_other	5.813
r_scangle_it	5.645
r_scangle_other	5.645
r_scbond_it	4.281
r_scbond_other	4.28
r_mcangle_other	3.021
r_mcangle_it	3.02
r_mcbond_it	2.456
r_mcbond_other	2.452
r_angle_other_deg	2.223
r_angle_refined_deg	1.72
r_nbd_other	0.274
r_nbd_refined	0.225
r_symmetry_nbd_other	0.217
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.097
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.075
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	4872
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	31

Software

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