7T9D

Crystal structure of dehaloperoxidase B in complex with -(-) limonene oxide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	MPEG 2000, ammonium sulfate, Na cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.657	α = 90
b = 66.492	β = 90
c = 68.34	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	1.66	34.193	97.3	0.975	15.3	3.7		31407

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	1.66	1.703			0.447

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	THROUGHOUT	3IXF	1.66	34.193	31407	1602	97.314	0.169	0.1659	0.2341	24.037

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]
-1.979			-1.295		3.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.897
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	17.554
r_rigid_bond_restr	11.791
r_scangle_it	7.093
r_lrange_it	7.077
r_lrange_other	7.031
r_scangle_other	6.741
r_scbond_it	5.788
r_scbond_other	5.592
r_dihedral_angle_1_deg	5.364
r_mcangle_other	4.213
r_mcangle_it	4.207
r_mcbond_it	3.499
r_mcbond_other	3.431
r_angle_refined_deg	1.83
r_angle_other_deg	1.568
r_symmetry_nbd_refined	0.298
r_nbd_other	0.275
r_nbd_refined	0.27
r_symmetry_nbd_other	0.229
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.136
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.061
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2132
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing