7C73 | pdb_00007c73

Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M CaCl2, 20% PEG 3350, tris-HCl, pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.88	α = 90
b = 79.93	β = 101.35
c = 75.05	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	2019-12-09	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 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	2.7	50	98	0.198	0.96	5	3.1		17274

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	96.8		0.96	0.536		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6LNV	2.7	47.577	16856	843	97.58	0.222	0.218	0.22	0.3063	0.31	35.678

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]
-0.042		-0.071	0.039		0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.68
r_dihedral_angle_3_deg	20.398
r_dihedral_angle_4_deg	16.2
r_lrange_it	10.506
r_lrange_other	10.499
r_dihedral_angle_1_deg	9.558
r_mcangle_it	3.644
r_mcangle_other	3.643
r_scangle_it	2.982
r_scangle_other	2.982
r_mcbond_it	2.061
r_mcbond_other	2.056
r_scbond_it	1.676
r_scbond_other	1.676
r_angle_refined_deg	1.664
r_angle_other_deg	1.224
r_nbd_other	0.271
r_nbd_refined	0.248
r_symmetry_xyhbond_nbd_refined	0.234
r_symmetry_nbd_other	0.209
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_refined	0.2
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4817
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	44

Software

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