7M1K | pdb_00007m1k

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

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	ammonium sulfate, sodium cacodylate, MPEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.145	α = 90
b = 66.697	β = 90
c = 68.028	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	1.79	37.122	94.22	0.994	18.9	3.5		24292

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	1.795	1.842			0.776

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	1.795	37.122	24292	1217	94.224	0.174	0.1713	0.18	0.2233	0.23	20.37

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]
1.311			0.085		-1.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.33
r_dihedral_angle_4_deg	19.104
r_dihedral_angle_3_deg	18.251
r_dihedral_angle_1_deg	5.968
r_lrange_it	4.652
r_lrange_other	4.612
r_scangle_it	2.911
r_scangle_other	2.911
r_scbond_it	1.942
r_scbond_other	1.937
r_angle_refined_deg	1.929
r_mcangle_it	1.761
r_mcangle_other	1.761
r_angle_other_deg	1.574
r_mcbond_it	1.138
r_mcbond_other	1.138
r_nbd_refined	0.252
r_symmetry_nbd_refined	0.241
r_nbd_other	0.219
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.151
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2137
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	144

Software

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