4GXW | pdb_00004gxw

Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	6.5	298	Protein (20 mM Hepes pH 7.5; Reservoir (0.2 M magnesium chloride, 0.1 M MES pH 6.5, 10% Peg4000); Cryoprotection (Reservoir, + 20% Diethylene glycol), sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.058	α = 90
b = 66.223	β = 93.64
c = 75.432	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX-225	MIRRORS	2012-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.3	75.28	99.5	0.073	0.073	10.9	3.5	175186	175186

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	1.3	1.37	98.3		0.567	0.567	1.3	2.9	25188

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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	3PAO	1.3	29.257	175099	175099	8755	99.41	0.1612	0.1612	0.1601	0.16	0.1814	0.18	RANDOM	16.8155

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	12.09
f_angle_d	1.081
f_chiral_restr	0.075
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5794
Nucleic Acid Atoms
Solvent Atoms	1309
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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.