7D52 | pdb_00007d52

Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BXI

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.98	α = 90
b = 85.08	β = 90
c = 98.93	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 PILATUS3 6M	mirror	2019-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	2.2	85	100	0.2	0.993	10.2	12		35006

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	2.2	2.27	99.9		0.99	0.967	3.1	11

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	3BXI	2.2	62.274	34747	1806	99.416	0.193	0.1902	0.19	0.2498	0.25	28.912

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]
0.031			-0.041		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.997
r_dihedral_angle_4_deg	16.894
r_dihedral_angle_3_deg	15.309
r_lrange_it	8.505
r_dihedral_angle_1_deg	7.161
r_scangle_it	4.385
r_mcangle_it	3.99
r_scbond_it	2.83
r_mcbond_it	2.412
r_angle_refined_deg	1.522
r_metal_ion_refined	0.321
r_nbtor_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.114
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	118

Software

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