8VKC | pdb_00008vkc

Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol

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	MPEG 2000, ammonium sulfate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.824	α = 90
b = 67.936	β = 90
c = 68.276	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		2022-09-25	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	2.03	30.43	93.05	0.98	12.4	3.7		16983

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	2.03	2.083			0.314

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	2.03	30.43	16983	841	93.047	0.16	0.1541	0.16	0.2745	0.28	28.825

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]
-0.758			0.632		0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.09
r_dihedral_angle_4_deg	25.425
r_dihedral_angle_3_deg	17.324
r_dihedral_angle_1_deg	6.015
r_lrange_it	5.998
r_lrange_other	5.995
r_scangle_it	5.628
r_scangle_other	5.62
r_mcangle_it	4.785
r_mcangle_other	4.784
r_scbond_it	4.494
r_scbond_other	4.458
r_mcbond_other	3.826
r_mcbond_it	3.825
r_rigid_bond_restr	2.193
r_angle_refined_deg	1.572
r_angle_other_deg	1.38
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.213
r_symmetry_nbd_other	0.193
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	127

Software

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