7DN6 | pdb_00007dn6

Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M Ammonium Iodide, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.913	α = 90
b = 79.69	β = 102.23
c = 76.965	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	MARRESEARCH	Mirror	2010-10-21	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	1.696	39.41	99.3	0.079	12	8.2		70470

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	1.696	1.74	93.9		0.59

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	3q9k	1.696	39.41	68757	3464	97.577	0.199	0.1974	0.2	0.2346	0.24	36.084

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]
0.008		0.033	-0.018		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.766
r_dihedral_angle_4_deg	14.896
r_dihedral_angle_3_deg	14.349
r_lrange_it	9.119
r_lrange_other	9.119
r_dihedral_angle_1_deg	7.19
r_scangle_it	5.312
r_scangle_other	5.311
r_mcangle_it	5.167
r_mcangle_other	5.163
r_scbond_it	3.504
r_scbond_other	3.503
r_mcbond_it	3.357
r_mcbond_other	3.346
r_chiral_restr_other	2.965
r_angle_other_deg	2.587
r_angle_refined_deg	1.75
r_nbd_other	0.254
r_symmetry_nbd_other	0.221
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_xyhbond_nbd_other	0.178
r_nbtor_refined	0.173
r_metal_ion_refined	0.108
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.034
r_gen_planes_other	0.016
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing