7VEV

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IPW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	20% PEG6000 0.2 M Calcium chloride 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.06	α = 75.859
b = 54.21	β = 66.897
c = 57.012	γ = 87.947

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		2020-01-31	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	1.498	50	99.9	0.055	27.4	2.9		79704

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	1.5	1.52			0.139

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	5IPW	1.498	26.133	79703	3892	94.765	0.168	0.1673	0.1879	11.403

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]
-0.478	-0.01	-0.078	0.162	-0.26	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.032
r_dihedral_angle_3_deg	12.231
r_dihedral_angle_4_deg	9.663
r_dihedral_angle_1_deg	6.122
r_lrange_it	4.282
r_lrange_other	4.175
r_scangle_it	3.132
r_scangle_other	3.132
r_angle_other_deg	2.258
r_scbond_it	1.942
r_scbond_other	1.942
r_mcangle_it	1.897
r_mcangle_other	1.897
r_angle_refined_deg	1.717
r_mcbond_it	1.219
r_mcbond_other	1.218
r_symmetry_xyhbond_nbd_other	0.295
r_nbd_other	0.228
r_nbd_refined	0.217
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.124
r_symmetry_nbd_refined	0.115
r_symmetry_nbtor_other	0.074
r_metal_ion_refined	0.067
r_symmetry_metal_ion_refined	0.055
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	507
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing