Experiment: 7REI

The crystal structure of nickel bound human ADO C18S C239S variant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S7E	customized ensenble

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.2 M LiSO4, 0.1 M Bis-Tris pH 5.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.881	α = 90
b = 95.764	β = 90
c = 117.614	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2021-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	99.4	0.11	0.114	0.032	5.7	12.7		29671			25.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	97.9		1.004	1.056	0.319	0.79		10.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	customized ensenble	1.78	47.62	1.36	29627	1990	99.03	0.1821	0.1801	0.2093	0.207	32.4678

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	13.564
f_angle_d	0.908
f_chiral_restr	0.056
f_plane_restr	0.008
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1921
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing