6L2J

Crystal structure of yak lactoperoxidase at 1.93 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6A4Y

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	42.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.85	α = 90
b = 78.92	β = 92.95
c = 67.75	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	0.98	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.93	53.84	100	0.066	0.078	0.04	0.996	14.3	3.7		42433

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98	100		0.218	0.258	0.136	0.935	5	3.5

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	6A4Y	1.933	53.837	42433	1503	99.991	0.147	0.1453	0.1979	19.698

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]
-0.029		-0.865	-0.207		0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.536
r_dihedral_angle_3_deg	17.149
r_dihedral_angle_4_deg	16.979
r_dihedral_angle_1_deg	8.117
r_lrange_it	6.992
r_lrange_other	6.991
r_mcangle_it	3.871
r_mcangle_other	3.863
r_scangle_it	3.284
r_scangle_other	3.284
r_mcbond_it	2.265
r_mcbond_other	2.244
r_scbond_it	2.032
r_scbond_other	2.031
r_angle_refined_deg	1.69
r_angle_other_deg	1.355
r_nbd_other	0.244
r_nbd_refined	0.241
r_chiral_restr_other	0.221
r_symmetry_nbd_refined	0.216
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.198
r_metal_ion_refined	0.197
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.01
r_symmetry_xyhbond_nbd_other	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4760
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	280

Software

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