4UWO | pdb_00004uwo

Native di-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumoniae has implications for drug binding.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y8B	PDB ENTRY 2Y8B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9.5		21% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 5K, 0.1 M CHES BUFFER AT PH 9.5 0.1 M MAGNESIUM FORMATE, 4% GLYCEROL, 0.1 M MAGNESIUM FORMATE AND 4% GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.634	α = 90
b = 67.882	β = 92.39
c = 40.231	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				2012-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	1.55	40	99.6	0.057	11.8	3.4		30529			18.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.64	97.1		0.618	1.9	3

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 2Y8B	1.555	21.967	1.37	30496	1541	99.56	0.1543	0.1526	0.15	0.1863	0.19

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	13.541
f_angle_d	1.229
f_chiral_restr	0.076
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1722
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	9

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
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.