6VDU | pdb_00006vdu

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX 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
2.21	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.174	α = 90
b = 67.901	β = 90
c = 67.905	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		2019-08-04	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	1.98	44.65	98.47	0.997	20.8	4.7		19407

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	1.98	2.03			0.777

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3IXF	1.98	44.65	19407	1040	98.473	0.201	0.1971	0.2051	0.2608	0.2681	30.44

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]
0.948			-0.639		-0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.373
r_dihedral_angle_4_deg	19.921
r_dihedral_angle_3_deg	18.053
r_lrange_it	6.044
r_lrange_other	6.017
r_dihedral_angle_1_deg	5.329
r_scangle_it	3.602
r_scangle_other	3.578
r_mcangle_other	2.609
r_mcangle_it	2.606
r_scbond_it	2.333
r_angle_refined_deg	2.328
r_scbond_other	2.317
r_mcbond_it	1.665
r_mcbond_other	1.65
r_angle_other_deg	1.554
r_nbd_refined	0.249
r_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.175
r_chiral_restr	0.141
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2066
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	131

Software

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