7T9E | pdb_00007t9e

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
2.13	42.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.996	α = 90
b = 66.742	β = 90
c = 67.859	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	1.57	36.81	93.5	0.999	22.67	4		35061

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	1.57	1.611			0.66

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	1.57	36.81	35061	1668	93.511	0.147	0.1432	0.15	0.2181	0.22	26.284

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]
-0.626			-2.316		2.942

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.579
r_dihedral_angle_4_deg	20.365
r_dihedral_angle_3_deg	18.507
r_lrange_it	6.644
r_lrange_other	6.59
r_scangle_it	6.379
r_scangle_other	6.33
r_scbond_it	5.658
r_scbond_other	5.474
r_dihedral_angle_1_deg	5.312
r_mcangle_other	4.83
r_mcangle_it	4.828
r_rigid_bond_restr	4.788
r_mcbond_it	4.279
r_mcbond_other	4.248
r_angle_refined_deg	1.923
r_angle_other_deg	1.572
r_nbd_refined	0.265
r_nbd_other	0.242
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.211
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.184
r_chiral_restr	0.115
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.084
r_xyhbond_nbd_other	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2135
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	135

Software

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