6VDX

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Manganese(III)- Porphyrin and Substrate Trichlorophenol

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
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.365	α = 90
b = 67.585	β = 90
c = 67.626	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	1.0000	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	1.53	44.642	99.83	1	28.1	4.5		41678			16.8

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	1.53	1.56			0.588

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	3xif	1.53	44.64	41678	2150	99.82	0.168	0.1645	0.2367	19.577

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]
-1.917			-0.551		2.468

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.586
r_dihedral_angle_4_deg	17.385
r_dihedral_angle_3_deg	16.745
r_rigid_bond_restr	7.871
r_dihedral_angle_1_deg	5.555
r_lrange_it	5.513
r_lrange_other	5.49
r_scangle_it	5.158
r_scangle_other	5.153
r_mcangle_it	4.235
r_mcangle_other	4.234
r_scbond_it	4.193
r_scbond_other	4.192
r_mcbond_it	3.418
r_mcbond_other	3.417
r_angle_refined_deg	2.583
r_angle_other_deg	1.61
r_symmetry_xyhbond_nbd_refined	0.305
r_nbd_other	0.266
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.237
r_symmetry_nbd_other	0.203
r_xyhbond_nbd_other	0.193
r_nbtor_refined	0.176
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.008
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2135
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	144

Software

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