6VD3 | pdb_00006vd3

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-bromophenol

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	0.2 M Ammonium Sulfate, MPEG 2000, 29-33%

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.656	α = 90
b = 67.432	β = 90
c = 67.547	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		2019-06-16	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	1.67	33.77	94.53	0.997	28.6	4.4		31197

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	1.67	1.71			0.746

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3IXF	1.67	33.77	31197	1546	94.531	0.169	0.1683	0.1884	17.85

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]
6.225			-2.455		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.578
r_dihedral_angle_4_deg	21.195
r_dihedral_angle_3_deg	18.391
r_dihedral_angle_other_2_deg	15.509
r_dihedral_angle_other_1_deg	12.796
r_dihedral_angle_1_deg	5.478
r_lrange_it	3.077
r_lrange_other	3.036
r_angle_refined_deg	1.73
r_angle_other_deg	1.457
r_scangle_it	1.253
r_scangle_other	1.234
r_mcangle_it	0.866
r_mcangle_other	0.866
r_scbond_it	0.816
r_scbond_other	0.804
r_mcbond_it	0.544
r_mcbond_other	0.542
r_nbd_refined	0.246
r_symmetry_nbd_refined	0.229
r_nbd_other	0.22
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.143
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2155
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	120

Software

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