6M7E

Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GN6

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.81	α = 90
b = 80.673	β = 103.07
c = 74.442	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	81	CCD	MARRESEARCH		2010-11-10	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	2.42	43.99	93.8	0.114	3.4	4.3		22380

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	2.42	2.48	96		0.314	2.4	6.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4GN6	2.42	43.953	22380	1146	94.053	0.188	0.1836	0.2687	57.688

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]
-0.257		-0.1	-0.025		0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.486
r_dihedral_angle_4_deg	17.604
r_dihedral_angle_3_deg	15.525
r_lrange_it	11.264
r_lrange_other	11.257
r_dihedral_angle_1_deg	7.814
r_scangle_it	6.267
r_scangle_other	6.267
r_mcangle_it	6.097
r_mcangle_other	6.086
r_scbond_it	4.174
r_scbond_other	4.173
r_mcbond_other	4.032
r_mcbond_it	4.031
r_angle_refined_deg	1.474
r_angle_other_deg	1.192
r_nbd_other	0.234
r_symmetry_xyhbond_nbd_refined	0.233
r_xyhbond_nbd_refined	0.231
r_nbd_refined	0.211
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.155
r_metal_ion_refined	0.126
r_symmetry_nbtor_other	0.079
r_chiral_restr_other	0.067
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4771
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	153

Software

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