6VD6

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-nitrophenol

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	0.2 M Ammonium Sulphate MPEG 2000, 29-33%

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.138	α = 90
b = 67.927	β = 90
c = 67.867	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		2019-04-04	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	1.56	37.3	94.48	0.998	29.4	3.8		35281

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	1.56	1.6			0.741

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	3IXF	1.563	37.3	37232	1951	94.483	0.185	0.1836	0.2161	18.272

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]
0.891			-0.444		-0.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.34
r_dihedral_angle_4_deg	26.497
r_dihedral_angle_3_deg	16.391
r_dihedral_angle_other_2_deg	11.652
r_dihedral_angle_1_deg	5.962
r_lrange_it	3.671
r_lrange_other	3.638
r_scangle_it	2.4
r_scangle_other	2.371
r_angle_refined_deg	2.001
r_angle_other_deg	1.636
r_scbond_it	1.584
r_scbond_other	1.561
r_mcangle_it	1.311
r_mcangle_other	1.311
r_mcbond_it	0.872
r_mcbond_other	0.871
r_dihedral_angle_other_1_deg	0.579
r_symmetry_nbd_refined	0.297
r_nbd_other	0.291
r_nbd_refined	0.252
r_nbtor_refined	0.192
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.135
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2159
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	124

Software

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