3KUN | pdb_00003kun

X-ray structure of the metcyano form of dehaloperoxidase from amphitrite ornata: evidence for photoreductive lysis of iron-cyanide bond

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EW6	PDB ENTRY 1EW6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	0.2 M AMMONIUM SULFATE, 28% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.252	α = 90
b = 66.55	β = 90
c = 68.713	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	MARMOSAIC 225 mm CCD		2007-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.26	35	99.1	0.053	218.6	3.5	70910	67355		2	11.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.26	1.29	95.6		0.324	0.324	2.6	3.3	4989

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EW6	1.26	35	2	70910	67355	3555	99.1	0.155	0.153	0.15	0.186	0.18	RANDOM	11.94

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]
0.12			0.02		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.165
r_dihedral_angle_4_deg	18.314
r_dihedral_angle_3_deg	14.54
r_dihedral_angle_1_deg	4.112
r_scangle_it	2.271
r_scbond_it	1.645
r_mcangle_it	1.14
r_angle_refined_deg	1.026
r_mcbond_it	0.706
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.165
r_dihedral_angle_4_deg	18.314
r_dihedral_angle_3_deg	14.54
r_dihedral_angle_1_deg	4.112
r_scangle_it	2.271
r_scbond_it	1.645
r_mcangle_it	1.14
r_angle_refined_deg	1.026
r_mcbond_it	0.706
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.128
r_symmetry_hbond_refined	0.122
r_chiral_restr	0.086
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	100

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.