6L5G | pdb_00006l5g

Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 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
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.82	α = 90
b = 84.71	β = 90
c = 99.04	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	2019-09-09	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	2.5	64.38	100	0.2	0.99	7.5	11.6		23901

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	2.5	2.6	100		0.845	0.818	2.7	11.3

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	3bxi	2.5	64.375	23818	1136	99.866	0.187	0.1846	0.19	0.2394	0.24	33.275

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]
-2.347			-1.193		3.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.693
r_dihedral_angle_3_deg	18.624
r_dihedral_angle_4_deg	15.566
r_lrange_it	8.936
r_lrange_other	8.935
r_dihedral_angle_1_deg	7.544
r_mcangle_other	4.876
r_mcangle_it	4.87
r_scangle_it	4.809
r_scangle_other	4.808
r_mcbond_it	2.899
r_mcbond_other	2.853
r_scbond_it	2.846
r_scbond_other	2.846
r_angle_refined_deg	1.587
r_angle_other_deg	1.229
r_symmetry_xyhbond_nbd_refined	0.551
r_symmetry_nbd_refined	0.321
r_metal_ion_refined	0.312
r_nbd_other	0.29
r_nbd_refined	0.238
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	147

Software

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