8Y9X | pdb_00008y9x

Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8K5M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	0.2 M Ammonium iodide, 20%(w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.35	α = 90
b = 80.332	β = 103.94
c = 73.391	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	298	CCD	MARMOSAIC 325 mm CCD		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	1.99	43.521	96.7	0.082	29.8	6.2		39294

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	1.99	2.05	77		0.31	4.3

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	8K5M	2	43.521	39294	1971	96.496	0.153	0.1506	0.16	0.1951	0.2	29.645

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]
-0.035		-0.01	0.055		-0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.321
r_dihedral_angle_3_deg	13.041
r_lrange_it	9.892
r_lrange_other	9.869
r_dihedral_angle_1_deg	6.873
r_dihedral_angle_2_deg	6.812
r_scangle_it	5.743
r_scangle_other	5.743
r_mcangle_other	5.335
r_mcangle_it	5.334
r_scbond_it	3.463
r_scbond_other	3.463
r_mcbond_it	3.283
r_mcbond_other	3.273
r_angle_refined_deg	1.684
r_angle_other_deg	0.783
r_symmetry_nbd_refined	0.347
r_nbd_other	0.313
r_nbd_refined	0.227
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.207
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.181
r_symmetry_nbtor_other	0.111
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_other	0.047
r_bond_other_d	0.013
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4742
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	205

Software

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