6L32 | pdb_00006l32

Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.30 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
2.49	50.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.7	α = 90
b = 84.71	β = 90
c = 98.75	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	CCD	MARRESEARCH	mirror	2019-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97947	RRCAT INDUS-2	PX-BL21

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	2.3	58.114	100	0.2	0.98	5.9	6.8		30425

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	2.3	2.39	99.9		0.85	0.88	1.9	6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3BXI	2.3	58.11	30367	663	99.947	0.191	0.1903	0.2	0.2442	0.25	27.013

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]
-1.087			-1.05		2.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.892
r_dihedral_angle_3_deg	19.183
r_dihedral_angle_4_deg	14.384
r_lrange_it	8.601
r_lrange_other	8.576
r_dihedral_angle_1_deg	7.694
r_mcangle_other	4.307
r_mcangle_it	4.305
r_scangle_it	4.019
r_scangle_other	4.019
r_mcbond_it	2.522
r_mcbond_other	2.505
r_scbond_other	2.464
r_scbond_it	2.463
r_angle_refined_deg	1.651
r_angle_other_deg	1.251
r_metal_ion_refined	0.371
r_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_other	0.221
r_symmetry_nbd_other	0.208
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_refined	0.174
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_other	0.138
r_symmetry_metal_ion_refined	0.086
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.007
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	4784
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	117

Software

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