8VKD

Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrocatechol

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
2.18	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.359	α = 90
b = 68.036	β = 90
c = 68.312	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		2023-03-03	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	1.4	44.411	94.65	1	27.5	4.2		51376

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	1.4	1.436			0.873

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	1.4	44.411	51376	2581	94.65	0.168	0.1658	0.2008	15.537

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]
-2.185			0.064		2.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.398
r_dihedral_angle_4_deg	20.611
r_dihedral_angle_3_deg	16.673
r_rigid_bond_restr	8.484
r_dihedral_angle_1_deg	5.715
r_lrange_it	3.917
r_lrange_other	3.748
r_scangle_it	3.568
r_scangle_other	3.563
r_scbond_other	3.142
r_scbond_it	3.139
r_mcangle_it	2.668
r_mcangle_other	2.668
r_mcbond_it	2.356
r_mcbond_other	2.353
r_angle_refined_deg	1.998
r_angle_other_deg	1.662
r_nbd_refined	0.317
r_symmetry_nbd_refined	0.273
r_nbd_other	0.271
r_symmetry_xyhbond_nbd_refined	0.248
r_symmetry_nbd_other	0.203
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_other	0.114
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.008
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2183
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	153

Software

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