9D5W

Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	1.6 M Lithium sulfate, 150 mM Cacodylate pH 6.5, 1.0 % v/v 1,2 propanediol

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.044	α = 90
b = 105.816	β = 119.922
c = 118.124	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 PILATUS3 X 6M		2017-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	59.11	95.8	0.114	0.141	0.082	0.8764	7.4	2.9		107373

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			0.469	0.578	0.333	0.565	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	59.11	107297	5579	95.487	0.196	0.1938	0.2285	27.931

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]
-18.861		1.701	35.709		-16.849

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.337
r_dihedral_angle_3_deg	14.133
r_dihedral_angle_1_deg	4.161
r_lrange_it	3.215
r_lrange_other	3.2
r_mcangle_it	2.75
r_mcangle_other	2.749
r_scangle_it	1.847
r_scangle_other	1.846
r_mcbond_it	1.767
r_mcbond_other	1.767
r_angle_refined_deg	1.261
r_scbond_it	1.234
r_scbond_other	1.233
r_dihedral_angle_2_deg	0.787
r_angle_other_deg	0.579
r_symmetry_xyhbond_nbd_refined	0.24
r_metal_ion_refined	0.231
r_symmetry_nbd_other	0.219
r_nbd_other	0.203
r_xyhbond_nbd_refined	0.187
r_nbd_refined	0.181
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.114
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15930
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
HKL-3000	phasing
MOLREP	phasing