6KY7

Crystal structure of yak lactoperoxidase at 2.27 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
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.08	α = 90
b = 80.64	β = 102.8
c = 76.13	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	mirror	2019-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97947	RRCAT INDUS-2	PX-BL21

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	2.27	52.792	100	0.084	0.994	7.6	3.8		29600

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.34	100		0.663	0.806	1.3	3.8

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	3BXI	2.27	52.79	29579	1020	99.976	0.198	0.1955	0.2663	54.465

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]
-1.586		3.455	-3.931		3.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.897
r_dihedral_angle_3_deg	18.817
r_dihedral_angle_4_deg	17.242
r_lrange_it	11.53
r_lrange_other	11.53
r_dihedral_angle_1_deg	7.875
r_mcangle_other	6.436
r_mcangle_it	6.435
r_scangle_other	5.81
r_scangle_it	5.806
r_mcbond_it	4.236
r_mcbond_other	4.195
r_scbond_it	3.843
r_scbond_other	3.827
r_angle_refined_deg	1.593
r_angle_other_deg	1.208
r_symmetry_nbd_refined	0.292
r_nbd_other	0.286
r_symmetry_xyhbond_nbd_refined	0.268
r_xyhbond_nbd_refined	0.231
r_nbd_refined	0.211
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.169
r_chiral_restr_other	0.139
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.083
r_metal_ion_refined	0.071
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4763
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	143

Software

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