7VEW

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

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	7.2	293	22% PEG3000 0.15 M Potassium sodium tartrate 0.1 M HEPES 23.4 mM Unsaturated trigalacturonic acid

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.687	α = 90
b = 83.657	β = 101.036
c = 148.521	γ = 90

Symmetry
Space Group	P 1 21 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 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	1.9	48.6	99.5	0.086	11.3	5.77		108404

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	1.9	2.02			0.645

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	1.92	48.591	105761	5288	99.894	0.211	0.2096	0.2324	34.749

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]
5.528		1.119	-3.394		-2.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.885
r_dihedral_angle_4_deg	13.681
r_dihedral_angle_3_deg	12.902
r_dihedral_angle_1_deg	6.282
r_lrange_other	3.752
r_lrange_it	3.75
r_scangle_it	3.509
r_scangle_other	3.509
r_scbond_it	2.757
r_scbond_other	2.756
r_mcangle_other	2.405
r_mcangle_it	2.402
r_angle_other_deg	2.211
r_mcbond_it	1.966
r_mcbond_other	1.963
r_angle_refined_deg	1.73
r_nbd_other	0.373
r_nbd_refined	0.227
r_symmetry_nbd_other	0.222
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.165
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_symmetry_xyhbond_nbd_other	0.097
r_symmetry_xyhbond_nbd_refined	0.084
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.034
r_bond_refined_d	0.014
r_gen_planes_other	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9692
Nucleic Acid Atoms
Solvent Atoms	479
Heterogen Atoms	152

Software

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