7DMR | pdb_00007dmr

Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.20 A resolution

X-RAY DIFFRACTION

---

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
2.53	51.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.24	α = 90
b = 85.31	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	64.61	99.9	0.2	0.993	9.1	12		35146

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	99.2		0.914	0.764	2.7	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	64.606	35048	1815	99.71	0.192	0.1896	0.2	0.2427	0.25	30.78

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]
-0.054			0.09		-0.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.867
r_dihedral_angle_4_deg	15.894
r_dihedral_angle_3_deg	14.729
r_lrange_it	8.718
r_lrange_other	8.717
r_dihedral_angle_1_deg	7.456
r_scangle_it	4.038
r_scangle_other	4.038
r_mcangle_other	3.931
r_mcangle_it	3.93
r_scbond_it	2.512
r_scbond_other	2.511
r_mcbond_it	2.372
r_mcbond_other	2.355
r_angle_refined_deg	1.574
r_angle_other_deg	1.29
r_metal_ion_refined	0.419
r_nbd_other	0.258
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.167
r_symmetry_nbd_refined	0.119
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	118

Software

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