4YJ6 | pdb_00004yj6

The Crystal Structure of a Bacterial Aryl Acylamidase Belonging to the Amidase signature (AS) enzymes family

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F2A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295.15	1.2 M NaH2PO4/0.8 M K2HPO4, 0.1 M CAPS pH 10.5, 0.2 M Li2SO4, 0.1 M ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.76	α = 90
b = 75.76	β = 90
c = 214	γ = 90

Symmetry
Space Group	P 41 21 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	ADSC QUANTUM 315r		2010-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	1.0	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	43.7	100	21.6	15.4		69651

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	NONE	2F2A	1.7	43.7	68225	1965	98.11	0.1553	0.1549	0.15	0.1679	0.17

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]
2.8825			2.8825		-5.7651

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.205
f_angle_d	1.454
f_chiral_restr	0.103
f_bond_d	0.014
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3708
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
MOSFLM	data scaling
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.