8VZR | pdb_00008vzr

Crystal structure of dehaloperoxidase A in complex with substrate 4-bromo-o-cresol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	MPEG2000, ammonium sulfate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.404	α = 90
b = 67.756	β = 90
c = 68.169	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		2022-11-03	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	1.64	37.14	99.79	0.987	30.8	9.3		33787

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	1.64	1.682			0.712

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	PDB entry 2QFK	1.64	37.136	33787	1678	99.787	0.158	0.1559	0.17	0.2044	0.22	19.16

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]
0.435			-0.47		0.035

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.336
r_dihedral_angle_6_deg	15.753
r_dihedral_angle_1_deg	5.358
r_dihedral_angle_2_deg	4.581
r_rigid_bond_restr	3.845
r_lrange_it	2.058
r_lrange_other	2.034
r_angle_refined_deg	1.649
r_scangle_it	1.384
r_scangle_other	1.382
r_mcangle_it	1.196
r_mcangle_other	1.196
r_scbond_it	1.095
r_scbond_other	1.092
r_mcbond_it	0.96
r_mcbond_other	0.958
r_angle_other_deg	0.614
r_nbd_other	0.339
r_nbd_refined	0.325
r_symmetry_nbd_refined	0.325
r_symmetry_nbd_other	0.24
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_other	0.117
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	175

Software

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