8AJS

Crystal structure of the F324A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.844	α = 90
b = 134.962	β = 106.043
c = 109.393	γ = 90

Symmetry
Space Group	C 1 2 1

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		2021-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97625	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.68	105.921	99.6	0.064	0.998	11.76	5.319		280732

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	1.68	1.78	98.5		0.56	1.02

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	6F3M	1.68	105.921	280727	1039	99.656	0.151	0.1509	0.1778	39.342

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]
-0.701		-0.384	-0.403		1.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.523
r_dihedral_angle_3_deg	13.459
r_dihedral_angle_4_deg	12.92
r_dihedral_angle_1_deg	7.456
r_lrange_it	5.799
r_lrange_other	5.586
r_scangle_it	4.066
r_scangle_other	4.066
r_scbond_it	2.789
r_scbond_other	2.789
r_mcangle_it	2.09
r_mcangle_other	2.09
r_mcbond_it	1.606
r_mcbond_other	1.606
r_angle_other_deg	1.399
r_angle_refined_deg	1.382
r_symmetry_xyhbond_nbd_other	0.238
r_nbd_refined	0.221
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.157
r_nbd_other	0.135
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.076
r_symmetry_nbd_refined	0.076
r_metal_ion_refined	0.074
r_ncsr_local_group_3	0.063
r_ncsr_local_group_6	0.063
r_ncsr_local_group_5	0.059
r_ncsr_local_group_1	0.058
r_ncsr_local_group_2	0.058
r_ncsr_local_group_4	0.058
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14184
Nucleic Acid Atoms
Solvent Atoms	1689
Heterogen Atoms	264

Software

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