7DAO | pdb_00007dao

Crystal structure of native yak lactoperoxidase at 2.28 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7D52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.05M potassium fluoride, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.162	α = 90
b = 85.242	β = 90
c = 96.443	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9677	ESRF	BM30A

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	2.28	42.621	99	0.15	0.99	7	7		30344			42.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.34	93		0.99	0.79	2.28

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	7D52	2.28	42.62	30343	770	98.513	0.176	0.1742	0.17	0.2434	0.24	50.639

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]
-3.004			-0.967		3.971

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.665
r_dihedral_angle_4_deg	17.247
r_dihedral_angle_3_deg	16.748
r_lrange_it	13.924
r_scangle_it	7.46
r_mcangle_it	6.966
r_dihedral_angle_1_deg	6.836
r_scbond_it	4.936
r_mcbond_it	4.387
r_angle_refined_deg	1.533
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.27
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.117
r_metal_ion_refined	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	116

Software

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