8DOJ

Dehaloperoxidase B in complex with 3,3'-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
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.595	α = 90
b = 67.374	β = 90
c = 67.647	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	PIXEL	DECTRIS EIGER X 16M		2021-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	1.3	33.85	91.24	0.994	27.88	3.4		62722

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	1.3	1.334			0.645

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	1.3	33.846	62722	3109	91.24	0.148	0.1455	0.1889	16.493

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]
-1.641			1.149		0.492

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.46
r_dihedral_angle_3_deg	15.706
r_dihedral_angle_2_deg	9.13
r_rigid_bond_restr	6.3
r_dihedral_angle_1_deg	5.761
r_scangle_other	5.219
r_scangle_it	5.216
r_lrange_it	4.865
r_lrange_other	4.755
r_scbond_other	4.696
r_scbond_it	4.69
r_mcangle_other	3.236
r_mcangle_it	3.235
r_mcbond_it	2.642
r_mcbond_other	2.642
r_angle_refined_deg	1.794
r_angle_other_deg	0.663
r_nbd_refined	0.271
r_nbd_other	0.203
r_nbtor_refined	0.198
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.181
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_other	0.034
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2145
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	122

Software

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