9DK2 | pdb_00009dk2

Lexapeptide dehydratase complex LxmKY, 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 solved LxmKY apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291.15	0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.716	α = 90
b = 120.661	β = 90
c = 152.767	γ = 90

Symmetry
Space Group	P 2 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		2022-03-13	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	2.5	49.282	100	0.221	0.239	0.089	0.99	7.2	13.4		37827

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	2.5	2.6	100		4.278	4.619	1.735	0.623		1.1

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	2.5	49.282	37783	1916	99.947	0.227	0.2243	0.2271	0.2676	0.273	70.592

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]
-3.765			4.385		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.932
r_dihedral_angle_3_deg	15.422
r_dihedral_angle_2_deg	13.782
r_lrange_other	12.081
r_lrange_it	12.079
r_mcangle_it	9.238
r_mcangle_other	9.237
r_scangle_it	9.115
r_scangle_other	9.114
r_mcbond_it	6.27
r_mcbond_other	6.261
r_scbond_it	6.226
r_scbond_other	6.224
r_dihedral_angle_1_deg	6.092
r_chiral_restr_other	1.537
r_angle_refined_deg	1.378
r_angle_other_deg	0.813
r_nbd_other	0.257
r_symmetry_nbd_other	0.231
r_nbd_refined	0.228
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.114
r_symmetry_xyhbond_nbd_refined	0.085
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.06
r_bond_refined_d	0.014
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4757
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	48

Software

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