8AJW

Crystal structure of the Q65N 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
2.41	48.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.503	α = 90
b = 133.618	β = 103.18
c = 100.865	γ = 90

Symmetry
Space Group	P 1 21 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		2021-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	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	1.819	79.133	99.7	0.097	0.999	12.05	6.87		171257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.819	1.917			0.144	0.156	0.683	1.11

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	1.819	79.133	171243	1285	99.703	0.16	0.1596	0.1941	36.188

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]
-1.157		-2.189	2.397		-0.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.748
r_dihedral_angle_4_deg	15.589
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_1_deg	7.558
r_lrange_it	4.908
r_lrange_other	4.771
r_scangle_it	2.811
r_scangle_other	2.783
r_scbond_it	1.919
r_scbond_other	1.894
r_mcangle_it	1.872
r_mcangle_other	1.872
r_angle_refined_deg	1.378
r_angle_other_deg	1.35
r_mcbond_it	1.326
r_mcbond_other	1.326
r_nbd_other	0.317
r_symmetry_nbd_refined	0.291
r_nbd_refined	0.213
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.078
r_ncsr_local_group_3	0.067
r_ncsr_local_group_5	0.067
r_ncsr_local_group_6	0.067
r_ncsr_local_group_1	0.066
r_ncsr_local_group_2	0.066
r_ncsr_local_group_4	0.066
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14224
Nucleic Acid Atoms
Solvent Atoms	1324
Heterogen Atoms	279

Software

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