6KZN

Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor X2

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M magnesium formate dihydrate, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.96	α = 90
b = 79.15	β = 138.4
c = 77.74	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS3 S 6M		2017-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00	Photon Factory	BL-5A

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	1.5	55.46	99.6	0.079	13.7	5.2		65271

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	1.5	1.58	100		0.16		5.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4nq2	1.5	39.606	65267	3385	99.591	0.157	0.1552	0.1829	12.08

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]
0.325		0.007	-0.621		0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.557
r_dihedral_angle_4_deg	22.378
r_dihedral_angle_3_deg	13.331
r_dihedral_angle_1_deg	7.602
r_lrange_it	4.709
r_lrange_other	4.709
r_scangle_it	3.222
r_scangle_other	3.222
r_dihedral_angle_other_3_deg	2.297
r_scbond_it	2.18
r_scbond_other	2.18
r_mcangle_other	2.099
r_mcangle_it	2.098
r_angle_refined_deg	1.45
r_angle_other_deg	1.425
r_mcbond_other	1.364
r_mcbond_it	1.361
r_nbd_other	0.225
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.204
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.095
r_metal_ion_refined	0.088
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3494
Nucleic Acid Atoms
Solvent Atoms	567
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing