8ZXG | pdb_00008zxg

Crystal structure of Paraoxonase from Bacillus sp. strain S3wahi

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, SITTING DROP		293.15	0.1 M MES monohydrate pH 6.5 1.6 M Magensium sulfate heptahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.823	α = 90
b = 77.823	β = 90
c = 135.266	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	DECTRIS EIGER X 16M		2024-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.494	39.01	100	0.043	0.044	0.012	29.4	13.3		67871		2	26.21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.494	1.52	99.25		2.083	2.164	0.579		13.47

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	AlphaFold	1.494	39.01	67871		99.901	0.185	0.183	0.1854	0.195	0.1844	34.89

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]
0.739			0.739		-1.477

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	42.963
r_lrange_other	42.943
r_scangle_it	18.591
r_scangle_other	18.586
r_mcangle_it	16.784
r_mcangle_other	16.784
r_dihedral_angle_3_deg	16.261
r_dihedral_angle_6_deg	14.867
r_dihedral_angle_2_deg	14.491
r_scbond_other	14.28
r_scbond_it	14.276
r_mcbond_it	12.159
r_mcbond_other	12.148
r_dihedral_angle_1_deg	7.029
r_rigid_bond_restr	5.508
r_angle_refined_deg	1.959
r_symmetry_nbd_refined	1.119
r_xyhbond_nbd_other	0.999
r_symmetry_xyhbond_nbd_refined	0.805
r_angle_other_deg	0.755
r_nbd_other	0.728
r_nbd_refined	0.234
r_symmetry_nbd_other	0.23
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2365
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	102

Software

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