4J9T | pdb_00004j9t

Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	6.5	277	protein buffer: 10 mM Tris HCl (pH 8). Precipitation cocktail: 100 MM NA CACODYLATE (PH 6.5), 5 mM FeCl2, 15% PEG 3350 Microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	38.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.163	α = 90
b = 79.677	β = 90
c = 83.777	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MAR CCD 165 mm	mirrors	2012-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97012	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.4	31.021	99.9	0.059	0.041	29.2	6.1		61532			11.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	99.7		0.42	0.405	4.9	4.9	6060

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EUU	1.4	31.021	1.3	1.34	61546	61460	6183	99.86	0.1394	0.1382	0.1349	0.12	0.1662	0.16	RANDOM

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]
-1.2254			0.8007		0.4246

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.698
f_angle_d	1.148
f_chiral_restr	0.069
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2675
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	7

Software

Software
Software Name	Purpose
PHENIX	refinement
COMO	phasing
XTALVIEW	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

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.