7C75

Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6L3Z

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.91	α = 90
b = 84.83	β = 90
c = 98.56	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 PILATUS 2M	mirror	2019-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	2.7	64.3	99.3	0.2	0.09	0.97	7.1	9.9		18790

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	2.7	2.77	97.6		1.05	0.34	0.83	2.8	9.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6L3Z	2.7	64.295	18789	893	98.931	0.197	0.193	0.2675	25.515

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]
0.061			0.172		-0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.907
r_dihedral_angle_3_deg	19.104
r_dihedral_angle_4_deg	15.146
r_dihedral_angle_1_deg	8.188
r_lrange_it	8.134
r_lrange_other	8.07
r_mcangle_other	4.476
r_mcangle_it	4.472
r_scangle_it	3.675
r_scangle_other	3.674
r_mcbond_it	2.585
r_mcbond_other	2.549
r_scbond_other	2.098
r_scbond_it	2.097
r_angle_refined_deg	1.648
r_angle_other_deg	1.192
r_symmetry_xyhbond_nbd_refined	0.332
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.214
r_nbd_other	0.211
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.167
r_symmetry_nbd_refined	0.163
r_symmetry_xyhbond_nbd_other	0.108
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4784
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	89

Software

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