9IT8

Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8ING

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	0.2M AMMONIUM IODIDE, 21% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.048	α = 90
b = 80.503	β = 102.849
c = 75.951	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	100	PIXEL	DECTRIS EIGER2 X 9M		2023-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	74.05	99.6	0.068	0.094	0.973	7.2	3.4		45886

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	95.2		0.763	0.725	0.658	0.9	3.5

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	1.954	74.049	45840	1357	99.496	0.19	0.1884	0.2474	53.701

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]
-1.108		1.371	-2.794		2.968

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.372
r_dihedral_angle_3_deg	14.311
r_lrange_it	12.545
r_lrange_other	12.544
r_dihedral_angle_1_deg	7.355
r_scangle_it	7.282
r_scangle_other	7.281
r_mcangle_it	7.168
r_mcangle_other	7.167
r_dihedral_angle_2_deg	5.969
r_mcbond_it	4.715
r_mcbond_other	4.694
r_scbond_it	4.614
r_scbond_other	4.613
r_chiral_restr_other	2.966
r_angle_refined_deg	1.727
r_angle_other_deg	1.508
r_nbd_other	0.238
r_nbd_refined	0.224
r_symmetry_nbd_other	0.216
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.207
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.098
r_symmetry_xyhbond_nbd_other	0.091
r_chiral_restr	0.086
r_gen_planes_other	0.026
r_gen_planes_refined	0.012
r_bond_refined_d	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4771
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	199

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing