6XJ0 | pdb_00006xj0

Crystal structure of multi-copper oxidase from Pediococcus pentosaceus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	Crystallization screening accomplished using combinatorial crystallization strategy. Separate libraries of precipitants, buffers, and additives were combinatorially combined with protein (11 mg/mL protein in 10 mM Tris-HCL pH 7.0) in situ on the crystallization plate. Final concentrations of mother liquor: Buffer: 83 mM Sodium Citrate pH 4.0 Additives: 670 mM lithium sulfate, 8 mM L-glutamine, 8 mM L-Aspartic acid, 8 mM glycine, 8 mM trans-4-hydroxy-L-proline. Reservoir solution:Precipitant: 2 M lithium sulfate Crystals only grow on Mylar surface (many surfaces were tested).

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.37	α = 90
b = 127.37	β = 90
c = 75.27	γ = 120

Symmetry
Space Group	P 32 2 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	2.34	110.31	99.4	0.335	0.955	4.47	4.73		29876

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	2.34	2.4	96.3		0.707	0.622

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.34	110.31	28375	1483	99.36	0.18399	0.18192	0.19	0.22256	0.22	RANDOM	29.107

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]
0.27	0.13		0.27		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.751
r_dihedral_angle_4_deg	19.233
r_dihedral_angle_3_deg	15.722
r_long_range_B_refined	7.754
r_dihedral_angle_1_deg	7.537
r_long_range_B_other	7.445
r_scangle_other	4.759
r_mcangle_it	3.146
r_mcangle_other	3.146
r_scbond_it	2.957
r_scbond_other	2.951
r_mcbond_other	2.058
r_mcbond_it	2.057
r_angle_refined_deg	1.856
r_angle_other_deg	0.993
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4032
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	7

Software

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