Experiment: 24GZ

Artificial Copper-binding trimeric protein 1 (Cu(I)TP6)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QWG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M Tris-HCl (pH 8.5) buffer containing 0.2 M trimethylamine N-oxide and 15% (w/v) PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.256	α = 90
b = 115.256	β = 90
c = 38.969	γ = 120

Symmetry
Space Group	P 3

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 S 9M		2024-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.979	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	28.81	97.95	0.988	11.53	10.5		23966			22.77

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.43			0.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.34	28.81	1.96	23891	1194	98.01	0.2114	0.2086	0.2071	0.2673	0.2651	24.74

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.0091
f_angle_d	0.424
f_chiral_restr	0.0407
f_bond_d	0.0019
f_plane_restr	0.0019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5626
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement