6VDR | pdb_00006vdr

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin 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 Sulphate MPEG 2000, 29-33%

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.401	α = 90
b = 67.641	β = 90
c = 67.646	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		2010-06-16	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	1.87	37.28	97.56	0.997	32.7	9.6		22564

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	1.87	1.91			0.997

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	1.87	37.28	21411	1153	97.561	0.206	0.2035	0.2502	28.394

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]
2.306			-1.04		-1.266

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.074
r_dihedral_angle_4_deg	22.676
r_dihedral_angle_3_deg	18.456
r_lrange_it	5.493
r_lrange_other	5.458
r_dihedral_angle_1_deg	4.902
r_scangle_it	3.991
r_scangle_other	3.932
r_mcangle_it	2.864
r_mcangle_other	2.863
r_scbond_it	2.736
r_scbond_other	2.553
r_angle_refined_deg	2.087
r_mcbond_it	2.027
r_mcbond_other	2.023
r_angle_other_deg	1.409
r_symmetry_xyhbond_nbd_refined	0.268
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.231
r_nbd_other	0.224
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.177
r_chiral_restr	0.176
r_symmetry_xyhbond_nbd_other	0.163
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2156
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	128

Software

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