7DE5

Crystal structure of yak lactoperoxidase at 1.55 A resolution.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M AMMONIUM IODIDE, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.91	α = 90
b = 78.98	β = 92.96
c = 67.82	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	MARMOSAIC 225 mm CCD		2019-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.55	44.53	98.4	0.107	0.067	0.99	7.6	3.3		81152

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	92.8		0.934	0.604	0.44	1.1

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	7BYZ	1.55	43.247	81012	1676	98.406	0.187	0.1865	0.226	19.578

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]
-0.008		-0.015	-0.005		0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.661
r_dihedral_angle_4_deg	15.935
r_dihedral_angle_3_deg	13.28
r_dihedral_angle_1_deg	7.408
r_lrange_it	5.791
r_lrange_other	5.79
r_mcangle_it	3.165
r_mcangle_other	3.165
r_scangle_it	3.095
r_scangle_other	3.094
r_scbond_it	2.01
r_scbond_other	2.01
r_mcbond_it	1.975
r_mcbond_other	1.934
r_angle_refined_deg	1.622
r_angle_other_deg	1.491
r_symmetry_metal_ion_refined	0.774
r_nbd_other	0.474
r_symmetry_nbd_refined	0.461
r_symmetry_xyhbond_nbd_refined	0.254
r_nbd_refined	0.215
r_xyhbond_nbd_other	0.199
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.172
r_symmetry_nbtor_other	0.097
r_metal_ion_refined	0.095
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_other	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	226

Software

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