6VOX

Crystal structure of multi-copper oxidase from Pseudomonas Parafulva

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	288	Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant: 0.0425 M BICINE pH 9.0 0.0425 M Sodium chloride 8.5% v/v Polyethylene glycol monomethyl ether 550 7.5% v/v Glycerol Solution was equilibrated against a reservoir of 60% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
5.8	78.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.35	α = 90
b = 170.35	β = 90
c = 131	γ = 120

Symmetry
Space Group	P 62 2 2

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 EIGER2 X 9M		2018-07-06	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	3.8	50	92.3	0.29	0.997	8.38	29.33		10690

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	3.8	3.9			2.578	0.258

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6VOW	3.8	30	10435	215	92.35	0.25802	0.2577	0.27404	RANDOM	195.234

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]
0.23	0.11		0.23		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	40.449
r_long_range_B_refined	40.447
r_dihedral_angle_2_deg	38.621
r_mcangle_it	27.386
r_mcangle_other	27.379
r_scangle_other	24.129
r_dihedral_angle_3_deg	22.836
r_dihedral_angle_4_deg	17.043
r_mcbond_other	16.926
r_mcbond_it	16.925
r_scbond_it	14.191
r_scbond_other	14.148
r_dihedral_angle_1_deg	12.096
r_angle_refined_deg	1.984
r_angle_other_deg	1.202
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3198
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

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