6LF7 | pdb_00006lf7

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	Sodium nitrate, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.881	α = 90
b = 80.731	β = 101.53
c = 75.139	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	80	CCD	MARRESEARCH	Mirror	2013-06-21	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)	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	1.79	27.214	96.38	0.099	0.94	7.2	8.3		56910

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.84	84.83		0.89	3.5	4.6

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	4N7A	1.794	27.214	56910	2871	96.382	0.234	0.231	0.24	0.2966	0.3	34.996

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]
-0.126		-0.012	0.273		-0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_4_deg	17.516
r_dihedral_angle_3_deg	16.787
r_lrange_it	8.209
r_lrange_other	8.151
r_dihedral_angle_1_deg	7.982
r_mcangle_it	4.464
r_mcangle_other	4.454
r_scangle_it	4.345
r_scangle_other	4.344
r_angle_other_deg	3.05
r_chiral_restr_other	2.965
r_mcbond_other	2.903
r_mcbond_it	2.898
r_scbond_it	2.808
r_scbond_other	2.807
r_angle_refined_deg	1.664
r_nbd_other	0.298
r_nbd_refined	0.254
r_symmetry_nbd_other	0.232
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.166
r_metal_ion_refined	0.143
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.043
r_bond_other_d	0.034
r_gen_planes_other	0.025
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4757
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	175

Software

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