6KMK | pdb_00006kmk

Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.828	α = 90
b = 80.42	β = 102.577
c = 75.823	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		2019-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.9795	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	54.515	99.2	0.112	0.96	7.2	3.4		27946

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38			0.495	1	2	3.3

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	THROUGHOUT	4NT3	2.3	54.46	27800	1401	98.725	0.248	0.2454	0.25	0.2951	0.29	40.537

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]
0.617		-1.481	-1.246		1.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.962
r_dihedral_angle_3_deg	16.741
r_dihedral_angle_4_deg	14.093
r_dihedral_angle_1_deg	7.863
r_lrange_other	7.101
r_lrange_it	7.099
r_mcangle_it	4.7
r_mcangle_other	4.7
r_scangle_it	4.328
r_scangle_other	4.328
r_mcbond_it	2.998
r_mcbond_other	2.993
r_scbond_it	2.763
r_scbond_other	2.761
r_angle_refined_deg	1.51
r_angle_other_deg	1.206
r_symmetry_metal_ion_refined	0.736
r_nbd_other	0.299
r_symmetry_xyhbond_nbd_refined	0.27
r_symmetry_nbd_refined	0.269
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_other	0.123
r_symmetry_nbtor_other	0.078
r_xyhbond_nbd_other	0.075
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4774
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
Aimless	data scaling
MOLREP	phasing