6TY6 | pdb_00006ty6

Variant W229D/F290W-2 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4) bound to 5(6)-nitrobenzotriazole (TS-analog)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FQK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	4	293	5.0 M Sodium formate, 100 mM AcNa pH 4-0

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.384	α = 90
b = 148.357	β = 90
c = 246.008	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	PIXEL	DECTRIS PILATUS3 6M		2019-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.8	48.48	98.56	0.089	0.1	0.045	0.997	10.77	5.2		130796			30.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	99.39		1.44	1.6	0.687	0.68	1.2	5.4

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5FQK	1.8	48.48	1.33	130626	6624	98.56	0.202	0.2006	0.2	0.2283	0.23	40.03

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	9.4267
f_angle_d	1.4386
f_chiral_restr	0.1015
f_bond_d	0.0186
f_plane_restr	0.0103

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6019
Nucleic Acid Atoms
Solvent Atoms	604
Heterogen Atoms	138

Software

Software
Software Name	Purpose
EDNA	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PHASER	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.