4PNX

Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OGW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.742	α = 90
b = 80.379	β = 103.5
c = 73.177	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARRESEARCH	mirror	2013-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.41	71.16	99.3	0.129	16.5		23328	23328

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.47	92.3		0.379	2.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3OGW	2.41	71.15	21994	1190	98.96	0.22302	0.21869	0.2991	RANDOM	38.347

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]
-0.4		-2.66	-2.53		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.054
r_dihedral_angle_3_deg	17.214
r_dihedral_angle_4_deg	14.439
r_dihedral_angle_1_deg	7.105
r_scbond_it	2.042
r_angle_refined_deg	1.619
r_mcangle_it	1.46
r_mcbond_it	0.785
r_chiral_restr	0.109
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.054
r_dihedral_angle_3_deg	17.214
r_dihedral_angle_4_deg	14.439
r_dihedral_angle_1_deg	7.105
r_scbond_it	2.042
r_angle_refined_deg	1.619
r_mcangle_it	1.46
r_mcbond_it	0.785
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4774
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement

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.