8AJU | pdb_00008aju

Crystal structure of the Q65A 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
2.79	55.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.132	α = 90
b = 85.925	β = 131.184
c = 125.568	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 PILATUS3 S 2M		2019-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918400	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.645	41.679	98.8	0.995	7.57	3.764		136460

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	1.65	1.74	95.9		0.543	1.14

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6F3M	1.645	41.679	136459	2101	99.115	0.167	0.1665	0.18	0.1983	0.21	30.907

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]
-0.635		0.034	0.057		0.205

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.264
r_dihedral_angle_4_deg	14.857
r_dihedral_angle_3_deg	13.082
r_dihedral_angle_1_deg	7.358
r_lrange_it	4.828
r_lrange_other	4.235
r_scangle_it	2.786
r_scangle_other	2.786
r_scbond_it	2.033
r_scbond_other	2.033
r_mcangle_it	1.926
r_mcangle_other	1.926
r_angle_refined_deg	1.629
r_mcbond_it	1.482
r_mcbond_other	1.482
r_angle_other_deg	1.466
r_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.168
r_nbd_other	0.167
r_symmetry_nbd_refined	0.121
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.058
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7088
Nucleic Acid Atoms
Solvent Atoms	1119
Heterogen Atoms	142

Software

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