8VSK

Crystal structure of Dehaloperoxidase A in complex with substrate 2,4-dibromophenol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	MPEG 2000, ammonium sulfate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.171	α = 90
b = 66.182	β = 90
c = 69.063	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		2022-09-25	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)	Rpim I (All)	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	1.515	36.691	99.62	0.086	0.979	21	8.8		41266

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	1.52	1.554			0.582

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	FREE R-VALUE	PDB entry 2QFK	1.515	36.691	41266	2050	99.616	0.182	0.1808	0.2052	16.331

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]
0.617			-0.408		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.364
r_dihedral_angle_4_deg	24.064
r_dihedral_angle_3_deg	16.973
r_dihedral_angle_1_deg	5.89
r_lrange_it	5.269
r_lrange_other	5.228
r_scangle_other	3.892
r_scangle_it	3.89
r_scbond_it	2.583
r_scbond_other	2.575
r_mcangle_it	2.012
r_mcangle_other	2.011
r_angle_refined_deg	1.764
r_angle_other_deg	1.578
r_mcbond_it	1.312
r_mcbond_other	1.306
r_symmetry_nbd_refined	0.315
r_nbd_refined	0.265
r_nbd_other	0.263
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_other	0.105
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
Epinorm	data reduction
SCALEPACK	data scaling
PHASER	phasing