8S6L | pdb_00008s6l

AzeD dehydratase of Pseudomonas aeruginosa

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, HANGING DROP	6.5	293	100 mM bis-Tris methane at pH 6.5 and 25% PEG-3350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.46	α = 90
b = 67.59	β = 90
c = 116.68	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 9M		2023-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980112	SOLEIL	PROXIMA 2

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	1.55	44.2	99.9	0.064	0.067	0.019	0.999	20	13.1		65281

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	1.55	1.59		98.7	1.079	1.122	0.303	0.769		13.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	44.2	61945	3261	99.86	0.14808	0.14568	0.1527	0.19447	0.1996	RANDOM	24.346

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]
-3.22			4.01		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.85
r_dihedral_angle_2_deg	8.404
r_dihedral_angle_1_deg	6.254
r_rigid_bond_restr	3.778
r_long_range_B_refined	3.454
r_long_range_B_other	3.279
r_scangle_other	2.649
r_mcangle_other	2.324
r_mcangle_it	2.323
r_scbond_it	1.969
r_scbond_other	1.968
r_mcbond_it	1.744
r_mcbond_other	1.744
r_angle_refined_deg	1.467
r_angle_other_deg	0.523
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3393
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	12

Software

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