7YWV | pdb_00007ywv

Eugenol oxidase from rhodococcus jostii: mutant S81H, D151E, A423M, H434Y, S394V, Q425S, I445D, S518P

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FXD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.06 M of MgCl 2/CaCl 2, 0.1 M Sodium Hepes/MOPS (acid), 20% Ethylene glycol, 20% PEG 8000.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.191	α = 90
b = 142.402	β = 100.41
c = 288.521	γ = 90

Symmetry
Space Group	I 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 2M		2021-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.965459	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	49.3	99.3	0.129	0.156	0.087	0.992	7.8	3.1		175685

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	100		1.264	1.514	0.823	0.466		3.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5FXD	2.4	49.3	166794	8819	99.21	0.2243	0.2223	0.22	0.2616	0.26	RANDOM	54.414

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]
3.46		4.86	-4.17		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.045
r_dihedral_angle_4_deg	18.596
r_dihedral_angle_3_deg	15.564
r_dihedral_angle_1_deg	6.854
r_angle_refined_deg	1.435
r_angle_other_deg	1.224
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.045
r_dihedral_angle_4_deg	18.596
r_dihedral_angle_3_deg	15.564
r_dihedral_angle_1_deg	6.854
r_angle_refined_deg	1.435
r_angle_other_deg	1.224
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32973
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	489

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.