6ZGM | pdb_00006zgm

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with the thiazolecarboxylate inhibitor ANT2681

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KO3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.96	α = 90
b = 78.178	β = 90
c = 79.659	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 EIGER2 XE 16M		2019-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.65	55.8	100	0.058	15.8	7.3		25911

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	1.65	1.74	100		0.73	2.6	7.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KO3	1.65	51.75	24701	1209	99.96	0.1799	0.1777	0.19	0.2254	0.23	RANDOM	27.312

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]
			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.446
r_dihedral_angle_4_deg	22.854
r_dihedral_angle_3_deg	13.786
r_dihedral_angle_1_deg	6.664
r_angle_refined_deg	1.774
r_angle_other_deg	1.458
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.446
r_dihedral_angle_4_deg	22.854
r_dihedral_angle_3_deg	13.786
r_dihedral_angle_1_deg	6.664
r_angle_refined_deg	1.774
r_angle_other_deg	1.458
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1749
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	39

Software

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