7Y3U | pdb_00007y3u

Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M cacl2, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.731	α = 90
b = 93.173	β = 91.2
c = 82.319	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	CCD	MARMOSAIC 225 mm CCD		2019-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97947	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	48.911	99	0.078	0.997	7.8	3.9		42834

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	98.7		0.806	0.638	1.2	3.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6LRN	2.5	48.864	42372	2105	98.924	0.222	0.219	0.22	0.2774	0.28	59.307

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]
-0.154		-0.015	-0.088		0.243

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.804
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_4_deg	14.488
r_lrange_it	12.434
r_lrange_other	12.434
r_dihedral_angle_1_deg	7.749
r_mcangle_it	7.285
r_mcangle_other	7.284
r_scangle_it	6.353
r_scangle_other	6.353
r_mcbond_it	4.569
r_mcbond_other	4.568
r_scbond_it	3.939
r_scbond_other	3.938
r_angle_other_deg	2.453
r_angle_refined_deg	1.506
r_symmetry_nbd_refined	0.241
r_symmetry_nbd_other	0.218
r_nbd_other	0.21
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.161
r_metal_ion_refined	0.146
r_ncsr_local_group_1	0.093
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_refined	0.057
r_bond_other_d	0.034
r_gen_planes_other	0.019
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9542
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	259

Software

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