7SJH

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

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	6.5	277	MPEG 2000, ammonium sulfate, Na cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.839	α = 90
b = 67.375	β = 90
c = 67.857	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	CCD	RAYONIX MX300-HS		2021-09-22	M	SINGLE WAVELENGTH

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

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	1.87	37.38	97.91	0.989	26.3	4.7		22814

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	1.87	1.918			0.846

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	1.87	37.38	22814	1139	97.906	0.186	0.1846	0.2232	34.874

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]
0.267			0.688		-0.955

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.069
r_dihedral_angle_4_deg	22.719
r_dihedral_angle_3_deg	17.371
r_lrange_it	7.913
r_lrange_other	7.906
r_dihedral_angle_1_deg	6.23
r_scangle_it	4.195
r_scangle_other	4.165
r_mcangle_other	3.006
r_mcangle_it	3.005
r_scbond_it	2.905
r_scbond_other	2.875
r_mcbond_it	2.143
r_mcbond_other	2.123
r_angle_refined_deg	1.838
r_angle_other_deg	1.498
r_nbd_refined	0.287
r_symmetry_nbd_other	0.227
r_nbd_other	0.222
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.113
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2132
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	152

Software

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