8AJT | pdb_00008ajt

Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F3M	6F3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Morpheus Crystallization Screen, Condition C12

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.71	α = 90
b = 134.561	β = 105.713
c = 108.091	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		2021-06-21	M	SINGLE WAVELENGTH

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

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	1.46	42.559	98.9	0.999	8.88	3.372		826623

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	1.46	1.55			0.316	0.53

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	1.499	42.559	386964	1045	99.832	0.152	0.1521	0.16	0.167	0.17	30.664

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]
-1.015		-0.809	-0.651		1.831

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.417
r_dihedral_angle_4_deg	15.182
r_dihedral_angle_3_deg	13.099
r_dihedral_angle_1_deg	7.375
r_lrange_it	5.702
r_lrange_other	5.513
r_scangle_it	3.466
r_scangle_other	3.451
r_scbond_it	2.409
r_scbond_other	2.377
r_mcangle_it	1.742
r_mcangle_other	1.742
r_angle_refined_deg	1.485
r_angle_other_deg	1.433
r_mcbond_it	1.281
r_mcbond_other	1.27
r_symmetry_nbd_refined	0.286
r_nbd_refined	0.225
r_nbd_other	0.219
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.139
r_metal_ion_refined	0.116
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.07
r_ncsr_local_group_4	0.066
r_symmetry_metal_ion_refined	0.065
r_ncsr_local_group_6	0.064
r_ncsr_local_group_5	0.062
r_ncsr_local_group_3	0.058
r_ncsr_local_group_2	0.051
r_gen_planes_refined	0.013
r_bond_refined_d	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14188
Nucleic Acid Atoms
Solvent Atoms	1575
Heterogen Atoms	379

Software

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