8ING

Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	Sodium nitrate, PEG

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.052	α = 90
b = 80.342	β = 102.82
c = 76.121	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	81	CCD	MARRESEARCH		2013-04-23	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)	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	1.98	35.329	99	0.96	32.4	4.3		43516

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	1.98	2.01			0.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.98	35.329	43516	2188	98.261	0.186	0.1829	0.2335	39.155

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]
0.012		-0.016	0.013		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.416
r_dihedral_angle_4_deg	14.723
r_dihedral_angle_3_deg	13.541
r_lrange_it	11.323
r_lrange_other	11.296
r_mcangle_it	7.351
r_mcangle_other	7.351
r_dihedral_angle_1_deg	7.077
r_scangle_it	5.643
r_scangle_other	5.642
r_mcbond_other	4.84
r_mcbond_it	4.838
r_scbond_it	3.717
r_scbond_other	3.716
r_chiral_restr_other	2.771
r_angle_other_deg	2.432
r_angle_refined_deg	1.681
r_metal_ion_refined	0.568
r_nbd_other	0.392
r_symmetry_nbd_refined	0.37
r_symmetry_xyhbond_nbd_other	0.256
r_symmetry_nbd_other	0.227
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.171
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.074
r_bond_other_d	0.034
r_gen_planes_other	0.023
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4761
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
AUTOMAR	data collection
BUCCANEER	model building