7SJE

Crystal structure of dehaloperoxidase B in complex with p-cymene

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
2.19	43.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.472	α = 90
b = 66.466	β = 90
c = 68.246	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	1.72	37.2	98.99	0.995	19.8	4.8		29111

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	1.72	1.765			0.751

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	1.72	37.198	29111	1522	98.993	0.18	0.1784	0.2107	17.746

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]
0.838			-0.367		-0.471

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.092
r_dihedral_angle_4_deg	24.973
r_dihedral_angle_3_deg	16.776
r_dihedral_angle_1_deg	6.321
r_lrange_it	5.243
r_lrange_other	5.193
r_scangle_it	2.48
r_scangle_other	2.467
r_angle_refined_deg	2
r_mcangle_it	1.664
r_mcangle_other	1.664
r_angle_other_deg	1.589
r_scbond_it	1.576
r_scbond_other	1.563
r_mcbond_it	1.077
r_mcbond_other	1.077
r_nbd_refined	0.277
r_symmetry_nbd_other	0.228
r_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
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	2133
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	118

Software

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