7C74 | pdb_00007c74

Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in CaCl2 at 2.73 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LO7

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.06	α = 90
b = 80.59	β = 101.31
c = 74.83	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	MARMOSAIC 325 mm CCD	mirror	2019-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97	RRCAT INDUS-2	PX-BL21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.73	53.01	99.9	0.123	0.079	0.96	6.5	3.5		16875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.73	2.8	100		0.314	0.197	0.94	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	6LO7	2.73	53.01	16834	826	99.704	0.2	0.1953	0.2	0.2919	0.29	31.186

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]
-0.079		0.029	-0.216		0.263

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.442
r_dihedral_angle_3_deg	17.401
r_dihedral_angle_4_deg	16.77
r_dihedral_angle_1_deg	8.548
r_lrange_it	7.636
r_lrange_other	7.556
r_mcangle_other	4.064
r_mcangle_it	4.062
r_scangle_it	3.006
r_scangle_other	3.006
r_mcbond_it	2.364
r_mcbond_other	2.346
r_scbond_other	1.683
r_scbond_it	1.682
r_angle_refined_deg	1.466
r_angle_other_deg	1.164
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_other	0.205
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.154
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.068
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
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	316
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing