7S0Y

Structures of TcdB in complex with Cdc42

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BVM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M sodium cacodylate (pH 6.6), 2.4 M ammonium sulfate, and 2.5% (v/v) Jeffamine M-600 (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.354	α = 90
b = 140.948	β = 90
c = 111.803	γ = 90

Symmetry
Space Group	C 2 2 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 16M		2018-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.79	111.8	100	0.063	0.999	16.9	6.7		24433

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.94			0.865	2.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BVM	2.79	92.4	23173	1241	99.93	0.21666	0.21437	0.25924	RANDOM	77.173

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]
-1.82			4.68		-2.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.721
r_dihedral_angle_4_deg	15.1
r_dihedral_angle_3_deg	14.801
r_long_range_B_other	9.517
r_long_range_B_refined	9.514
r_mcangle_other	6.996
r_mcangle_it	6.994
r_scangle_other	6.46
r_dihedral_angle_1_deg	6.35
r_mcbond_it	4.524
r_mcbond_other	4.512
r_scbond_it	4.198
r_scbond_other	4.124
r_angle_refined_deg	1.31
r_angle_other_deg	1.159
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5787
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	110

Software

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