6XIZ

Crystal structure of multi-copper oxidase from Pediococcus acidilactici

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10.0 mg/mL protein in 5 mM Tris-HCL pH 7.2 Mylar was initially used as the surface, resulting in thin polycrystalline needles. Changing the surface to COC (cyclic olefin copolymer) resulted in large high-quality single crystals.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.06	α = 90
b = 147.3	β = 98.55
c = 65.46	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	PIXEL	DECTRIS EIGER X 9M		2019-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9202	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.78	73.65	98.3	0.185	0.999	10.37	25.53		98773

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.82	77.6		0.4263	0.476	0.71

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	73.65	92098	4742	99.97	0.11624	0.1139	0.161	RANDOM	47.028

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]
0.44		1	-0.23		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.007
r_sphericity_free	29.463
r_sphericity_bonded	18.229
r_dihedral_angle_3_deg	18.097
r_dihedral_angle_4_deg	17.055
r_scangle_other	9.509
r_scbond_it	9.229
r_scbond_other	9.229
r_long_range_B_refined	8.301
r_long_range_B_other	8.226
r_dihedral_angle_1_deg	7.573
r_mcangle_other	6.614
r_mcangle_it	6.613
r_rigid_bond_restr	6.057
r_mcbond_it	5.978
r_mcbond_other	5.958
r_angle_refined_deg	2.579
r_angle_other_deg	1.275
r_chiral_restr	0.2
r_bond_refined_d	0.03
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7622
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	21

Software

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