9DK1 | pdb_00009dk1

Lexapeptide dehydratase complex LxmKY apo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A6THA0-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291.15	0.2 M sodium acetate trihydrate; 0.1 M Bis-Tris propane pH 7.5; 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.704	α = 90
b = 90.28	β = 90
c = 148.953	γ = 90

Symmetry
Space Group	P 21 21 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		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.954	Australian Synchrotron	MX2

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	2.4	48.62	100	0.434	0.45	0.118	0.996	8.6	27.3		31270

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	2.4	2.49			2.794	3.152	1.433	0.369		4.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.4	48.62	31211	1613	99.984	0.214	0.2114	0.2148	0.2654	0.2663	50.996

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]
0.368			1.13		-1.498

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.384
r_dihedral_angle_6_deg	16.207
r_dihedral_angle_2_deg	15.043
r_lrange_it	10.242
r_lrange_other	10.238
r_scangle_it	8.282
r_scangle_other	8.281
r_mcangle_it	7.29
r_mcangle_other	7.289
r_scbond_it	5.842
r_scbond_other	5.84
r_dihedral_angle_1_deg	5.627
r_mcbond_it	5.072
r_mcbond_other	5.058
r_chiral_restr_other	1.537
r_angle_refined_deg	1.496
r_angle_other_deg	0.902
r_symmetry_xyhbond_nbd_refined	0.457
r_symmetry_nbd_refined	0.255
r_symmetry_nbd_other	0.236
r_nbd_refined	0.212
r_nbd_other	0.201
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.13
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4796
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	17

Software

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