7WYJ | pdb_00007wyj

Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	Ammonium Iodide, PEG3350, pH6.8

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.99	α = 90
b = 79.93	β = 102.18
c = 76.31	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	MAR CCD 165 mm		2010-05-13	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)	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	1.89	35.301	99.94	0.09	0.94	13.5	4.3		50802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.94			0.341	0.89	5

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	7VIN	1.89	35.301	50802	2579	99.945	0.206	0.2031	0.21	0.258	0.26	34.526

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]
0.003		0.007	-0.013		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.447
r_dihedral_angle_4_deg	16.252
r_dihedral_angle_3_deg	15.35
r_lrange_it	8.545
r_lrange_other	8.544
r_dihedral_angle_1_deg	7.286
r_mcangle_it	5.035
r_mcangle_other	5.035
r_scangle_it	4.598
r_scangle_other	4.597
r_mcbond_it	3.158
r_mcbond_other	3.149
r_scbond_it	2.832
r_scbond_other	2.832
r_angle_refined_deg	1.605
r_angle_other_deg	1.325
r_symmetry_xyhbond_nbd_refined	0.264
r_nbd_other	0.263
r_nbd_refined	0.246
r_symmetry_nbd_other	0.211
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.169
r_metal_ion_refined	0.119
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	161

Software

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