7SJI | pdb_00007sji

Crystal structure of dehaloperoxidase B in complex with R-(+)-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
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.775	α = 90
b = 66.988	β = 90
c = 67.759	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	1.76	33.9	97.88	0.999	27.6	4.7		27041

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	1.76	1.806			0.784

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	THROUGHOUT	3IXF	1.76	33.9	27041	1255	97.882	0.196	0.1946	0.2	0.2323	0.24	35.759

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]
1.776			-0.601		-1.175

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.278
r_dihedral_angle_4_deg	20.945
r_dihedral_angle_3_deg	18.077
r_lrange_it	7.705
r_lrange_other	7.701
r_dihedral_angle_1_deg	5.844
r_scangle_it	4.034
r_scangle_other	4.025
r_mcangle_other	2.913
r_mcangle_it	2.912
r_scbond_it	2.731
r_scbond_other	2.719
r_mcbond_it	2.057
r_mcbond_other	2.056
r_angle_refined_deg	1.848
r_angle_other_deg	1.547
r_nbd_refined	0.271
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.185
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.104
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.087
r_symmetry_nbd_refined	0.075
r_chiral_restr_other	0.045
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2129
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	134

Software

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