4GVW | pdb_00004gvw

Three-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BFR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	6		Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:0.1M Ammonium Sulfate, 0.1M MES, 40% PEG 8000, microbatch under oil

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.644	α = 90
b = 62.052	β = 90
c = 107.067	γ = 90

Symmetry
Space Group	I 2 2 2

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	2012-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.979	NSLS	X4C

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	2.1	50	95.8	0.081	37	12.7		10802		-3	24.2

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	BALBES	THROUGHOUT	2BFR	2.113	41.427	1.34	10795	520	98.31	0.175	0.172	0.17	0.239	0.23	random	32.397

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]
-4.39			-3.212		7.603

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.144
f_angle_d	1.003
f_chiral_restr	0.073
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1456
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	21

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
msr165	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.