3NIU | pdb_00003niu

Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 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	4.8	280	0.2M Potassium dihydrogen phosphate 20%w/v PEG 3350, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 280K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.199	α = 79.93
b = 75.587	β = 77.86
c = 83.808	γ = 72.5

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	278	IMAGE PLATE	MARRESEARCH	MIRROR	2006-09-20	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	2.94	25	96	4		28536	28536

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2OJV	2.94	25	27191	25825	1366	94.99	0.24187	0.20069	0.19744	0.2	0.23171	0.27	RANDOM	19.774

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]
0.5	1.39	-0.36	-0.33	0.73	-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.837
r_dihedral_angle_4_deg	16.115
r_dihedral_angle_3_deg	14.614
r_dihedral_angle_1_deg	5.226
r_scangle_it	1.247
r_angle_refined_deg	1.093
r_scbond_it	0.664
r_mcangle_it	0.622
r_symmetry_hbond_refined	0.347
r_mcbond_it	0.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.837
r_dihedral_angle_4_deg	16.115
r_dihedral_angle_3_deg	14.614
r_dihedral_angle_1_deg	5.226
r_scangle_it	1.247
r_angle_refined_deg	1.093
r_scbond_it	0.664
r_mcangle_it	0.622
r_symmetry_hbond_refined	0.347
r_mcbond_it	0.346
r_symmetry_vdw_refined	0.309
r_nbtor_refined	0.302
r_nbd_refined	0.194
r_metal_ion_refined	0.158
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9514
Nucleic Acid Atoms
Solvent Atoms	464
Heterogen Atoms	340

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 R01GM157729.