8BNT

The DH domain of ARHGEF2 bound to RhoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D0N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	2.6 M sodium formate, 100 mM Tris

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.432	α = 90
b = 71.432	β = 90
c = 196.527	γ = 90

Symmetry
Space Group	P 43 21 2

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 EIGER2 XE 9M		2022-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9212	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.4	71.43	100	0.072	0.999	10.3	45.8		101036

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	99.9		3.132	0.403	0.7	22.9

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4D0N	1.4	57.845	100884	2000	99.972	0.131	0.1297	0.1751	19.506

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]
0.307			0.307		-0.614

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.665
r_dihedral_angle_3_deg	13.245
r_dihedral_angle_2_deg	8.248
r_scangle_it	6.091
r_scangle_other	6.091
r_scbond_it	5.737
r_scbond_other	5.602
r_dihedral_angle_1_deg	5.566
r_lrange_it	5.512
r_lrange_other	5.451
r_rigid_bond_restr	5.15
r_mcangle_it	3.547
r_mcangle_other	3.546
r_mcbond_other	2.91
r_mcbond_it	2.909
r_angle_refined_deg	1.64
r_angle_other_deg	0.609
r_nbd_refined	0.256
r_xyhbond_nbd_refined	0.244
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.172
r_nbd_other	0.171
r_symmetry_nbd_refined	0.155
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3427
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing