7VET | pdb_00007vet

Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in a closed 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		293	20% PEG3350 0.2 M Ammonium formate 0.0209 mM Polygalacturonic acid sodium

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.626	α = 103.034
b = 54.998	β = 97.4
c = 112.829	γ = 92.36

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 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	2.25	48.2	95.9	0.055	14.2	6.12		53456

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	2.25	2.39			0.109

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7VEV	2.25	43.53	53456	2673	95.957	0.211	0.2089	0.21	0.2512	0.25	28.387

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]
-0.471	-1.812	-0.299	-2.102	0.29	2.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.332
r_dihedral_angle_4_deg	14.146
r_dihedral_angle_3_deg	13.111
r_lrange_other	6.318
r_lrange_it	6.314
r_scangle_it	6.289
r_scangle_other	6.289
r_dihedral_angle_1_deg	6.204
r_scbond_it	5.593
r_scbond_other	5.592
r_mcangle_it	5.011
r_mcangle_other	5.011
r_mcbond_it	4.301
r_mcbond_other	4.301
r_angle_other_deg	2.24
r_angle_refined_deg	1.79
r_nbd_other	0.32
r_symmetry_nbd_other	0.222
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.206
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.13
r_xyhbond_nbd_other	0.129
r_symmetry_nbd_refined	0.116
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.074
r_bond_other_d	0.034
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9692
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms

Software

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