9G3A | pdb_00009g3a

Crystal Structure of the artificial protein METP in complex with cadmium ion at different temperature, 160 K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Same complex at 100 K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	drop containing 2.0 μL of 1:1 (v/v) mixture of protein solution (10 mg/mL, 7 mM DTT, 4 mM CdCl2) and 2.0 μL of precipitant buffer (0.1 M HEPES at pH 7.5, 1.4 M sodium citrate tribasic dihydrate) was equilibrated against 0.5 mL reservoir of precipitant buffer

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.384	α = 90
b = 56.338	β = 90
c = 19.191	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	160	PIXEL	DECTRIS PILATUS3 6M		2000-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.534	ELETTRA	11.2C

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	1.7	31.15	96.8	0.07	0.99	9.3	2.3		9670			13.05

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	1.7	1.8			0.15	0.952

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	31.15	1.41	1730		98.52	0.1597	0.1597	0.1601		15.96

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	16.0737
f_angle_d	1.036
f_chiral_restr	0.0493
f_plane_restr	0.0089
f_bond_d	0.0076

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	204
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
XPREP	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.