9DK3 | pdb_00009dk3

Lexapeptide dehydratase complex LxmKY, hydrolysed ATP bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Previously determined LxmKY apo structure

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 7.5 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.175	α = 90
b = 91.583	β = 90
c = 151.372	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	2.3	49.11	100	0.458	0.475	0.125	0.996	8.8	27.3		36800

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	2.3	2.38	100		0.41		28.2

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	46.753	36734	1804	99.978	0.211	0.2083	0.2121	0.2571	0.2559	61.266

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]
-0.657			2.016		-1.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.073
r_dihedral_angle_3_deg	15.78
r_dihedral_angle_2_deg	13.092
r_lrange_other	12.024
r_lrange_it	12.023
r_scangle_it	9.66
r_scangle_other	9.588
r_mcangle_it	8.852
r_mcangle_other	8.852
r_scbond_it	6.957
r_scbond_other	6.906
r_dihedral_angle_1_deg	6.316
r_mcbond_it	6.309
r_mcbond_other	6.278
r_angle_refined_deg	1.548
r_angle_other_deg	0.808
r_symmetry_xyhbond_nbd_refined	0.367
r_symmetry_nbd_other	0.23
r_nbd_other	0.229
r_nbd_refined	0.218
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_other	0.093
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4802
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	74

Software

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