8C0J

Structure of AmiB enzymatic domain bound to the EnvC LytM domain

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	290	Na Phosphate pH7.6

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 237.363	α = 90
b = 237.363	β = 90
c = 237.363	γ = 90

Symmetry
Space Group	I 41 3 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 EIGER X 16M		2022-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

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	3.38	59.34	100	0.088	0.998	9.9	78.2		16294			81

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	3.38	3.65			0.686	0.939	1.6

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	in silico model	3.381	50.005	16103	817	98.967	0.251	0.2492	0.2909	119.898

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	22.52
r_lrange_other	22.518
r_dihedral_angle_3_deg	18.895
r_mcangle_it	17.812
r_mcangle_other	17.809
r_scangle_other	17.101
r_scangle_it	17.076
r_dihedral_angle_6_deg	13.746
r_mcbond_it	12.02
r_mcbond_other	12.018
r_scbond_other	10.913
r_scbond_it	10.901
r_dihedral_angle_2_deg	8.99
r_dihedral_angle_1_deg	8.407
r_angle_refined_deg	1.405
r_angle_other_deg	0.496
r_symmetry_xyhbond_nbd_refined	0.262
r_nbd_refined	0.248
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.185
r_nbd_other	0.162
r_symmetry_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.102
r_ncsr_local_group_1	0.099
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_ext_dist_refined_b	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4045
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	12

Software

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