7M1J | pdb_00007m1j

Crystal structure of dehaloperoxidase B in complex with 2,6-dibromophenol

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		277	ammonium sulfite, sodium cacodylate, MPEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.756	α = 90
b = 66.594	β = 90
c = 68.283	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	1.0000	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	1.55	30.4	91.92	0.998	22.6	3.5		36705

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	1.554	1.594			0.868

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	1.554	30.4	36705	1785	91.919	0.149	0.1459	0.15	0.2057	0.21	21.048

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]
-3.913			1.75		2.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.063
r_dihedral_angle_4_deg	20.077
r_dihedral_angle_3_deg	16.127
r_rigid_bond_restr	7.736
r_scangle_other	7.534
r_scangle_it	7.521
r_lrange_it	7.296
r_lrange_other	7.269
r_scbond_other	6.575
r_scbond_it	6.567
r_dihedral_angle_1_deg	5.696
r_mcangle_it	4.674
r_mcangle_other	4.672
r_mcbond_it	3.921
r_mcbond_other	3.906
r_angle_refined_deg	1.953
r_angle_other_deg	1.624
r_nbd_refined	0.291
r_nbd_other	0.217
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.183
r_symmetry_nbd_refined	0.135
r_chiral_restr	0.109
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2123
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	111

Software

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