7SJD | pdb_00007sjd

Crystal structure of dehaloperoxidase B in complex with terpinolene

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	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.711	α = 90
b = 67.574	β = 90
c = 67.856	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		2021-07-31	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	1.7	37.383	98.52	0.996	30.3	4.6		30227

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	1.703	1.748			0.547

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	1.703	37.383	30227	1383	98.517	0.188	0.1859	0.19	0.2247	0.23	31.851

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]
1.603			-0.669		-0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.24
r_dihedral_angle_4_deg	22.055
r_dihedral_angle_3_deg	17.54
r_lrange_it	6.964
r_lrange_other	6.904
r_dihedral_angle_1_deg	6.061
r_scangle_it	3.442
r_scangle_other	3.438
r_mcangle_other	2.376
r_mcangle_it	2.375
r_scbond_it	2.247
r_scbond_other	2.242
r_angle_refined_deg	1.793
r_mcbond_it	1.602
r_mcbond_other	1.602
r_angle_other_deg	1.532
r_nbd_refined	0.284
r_symmetry_nbd_other	0.231
r_nbd_other	0.203
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.167
r_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.099
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
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	111
Heterogen Atoms	134

Software

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