6VD4 | pdb_00006vd4

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

X-RAY DIFFRACTION

---

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 Sulphate, MPEG 2000, 29-33%

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.867	α = 90
b = 68.078	β = 90
c = 67.631	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	1.95	30.42	99.42	0.995	12	2.4		20289

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	1.95	2.01			0.649

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	1.954	30.42	19160	1013	99.418	0.198	0.1952	0.2418	25.718

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]
0.16			-0.382		0.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.839
r_dihedral_angle_4_deg	25.075
r_dihedral_angle_3_deg	17.86
r_dihedral_angle_other_2_deg	16.685
r_dihedral_angle_other_1_deg	15.041
r_dihedral_angle_1_deg	6.107
r_lrange_it	5.002
r_lrange_other	4.991
r_scangle_it	2.113
r_scangle_other	2.097
r_angle_refined_deg	1.795
r_angle_other_deg	1.435
r_mcangle_it	1.389
r_mcangle_other	1.389
r_scbond_it	1.325
r_scbond_other	1.311
r_mcbond_it	0.876
r_mcbond_other	0.874
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.252
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_other	0.23
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.086
r_xyhbond_nbd_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_symmetry_xyhbond_nbd_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	122

Software

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