4JXI | pdb_00004jxi

Directed evolution and rational design of a de novo designed esterase toward improved catalysis. Northeast Structural Genomics Consortium (NESG) Target OR184

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U10	PDB ENTRY 3U10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	6	277	Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Potassium Bromide 0.1M,mMES 0.1M, PEG4000 40% (w/v), microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.201	α = 90
b = 90.122	β = 90
c = 137.349	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	ADSC QUANTUM 4		2012-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97942	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.23	50	100	0.124	18.8	5.3		38878		-3	20.5

Refinement

Statistics
Diffraction ID	Structure Solution 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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3U10	2.29	29.82	1.44	67776	3364	99.43	0.1686	0.1652	0.17	0.2323	0.23	19.997

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	14.309
f_angle_d	1.08
f_chiral_restr	0.072
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6532
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	24

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	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.