7VE3 | pdb_00007ve3

Structure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IKC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	Ammonium iodide, PEG 3350, pH6.8

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.942	α = 90
b = 80.179	β = 102.86
c = 76.122	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	2011-02-13	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)	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	2.7	43.974	98.1	0.07	46	4.2		17167

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	2.7	2.75	93		0.24	10

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	2IKC	2.7	43.974	17092	860	97.635	0.199	0.1947	0.1945	0.2769	0.277	68.42

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]
-0.164		-0.001	-0.284		0.406

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.154
r_dihedral_angle_4_deg	19.208
r_dihedral_angle_3_deg	17.459
r_lrange_it	13.467
r_mcangle_it	7.834
r_scangle_it	7.655
r_dihedral_angle_1_deg	7.336
r_scbond_it	5.234
r_mcbond_it	4.949
r_angle_refined_deg	1.459
r_symmetry_xyhbond_nbd_refined	0.342
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.118
r_metal_ion_refined	0.101
r_gen_planes_refined	0.007
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4806
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	62

Software

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