3NAK

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OJV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	280	0.2 M Ammonium Formate 20%w/v PEG 3350, PH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.991	α = 85.45
b = 72.272	β = 84.04
c = 83.652	γ = 75.89

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	MIRROR	2006-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.3	20	94.8			18655	18655

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.42	97		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2OJV	3.3	19.87	18592	17642	950	94.49	0.251	0.20772	0.20473	0.243	RANDOM	25.473

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]
1.8	2.32		-0.93	0.28	-2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.972
r_dihedral_angle_3_deg	17.466
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_1_deg	5.467
r_scangle_it	1.358
r_angle_refined_deg	1.191
r_scbond_it	0.742
r_mcangle_it	0.656
r_mcbond_it	0.365
r_symmetry_vdw_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.972
r_dihedral_angle_3_deg	17.466
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_1_deg	5.467
r_scangle_it	1.358
r_angle_refined_deg	1.191
r_scbond_it	0.742
r_mcangle_it	0.656
r_mcbond_it	0.365
r_symmetry_vdw_refined	0.314
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.306
r_metal_ion_refined	0.241
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9514
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	398

Software

Software
Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
AUTOMAR	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 R01GM133198.