8DOI

Dehaloperoxidase B in complex with 2,2'-Biphenol

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	MPEG 2000, Ammonium Sulfate, Sodium Cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.239	α = 90
b = 67.702	β = 90
c = 68.038	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		2021-04-18	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	1.93	37.32	99.59	1	13.24	4.5		21108

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	1.93	1.98			0.542

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	1.93	37.318	21108	1005	99.59	0.177	0.174	0.2291	21.484

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]
-0.217			0.487		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.27
r_dihedral_angle_4_deg	21.171
r_dihedral_angle_3_deg	16.816
r_lrange_it	8.788
r_lrange_other	8.773
r_dihedral_angle_1_deg	5.704
r_scangle_it	2.768
r_scangle_other	2.768
r_angle_refined_deg	1.912
r_scbond_it	1.87
r_scbond_other	1.869
r_mcangle_other	1.781
r_mcangle_it	1.78
r_angle_other_deg	1.551
r_mcbond_it	1.145
r_mcbond_other	1.141
r_nbd_refined	0.268
r_symmetry_nbd_refined	0.255
r_nbd_other	0.247
r_symmetry_xyhbond_nbd_refined	0.209
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_other	0.16
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.013
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	2133
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	199

Software

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