8I52

Crystal structure of VIM-2 metallo-beta-lactamase in complex with 10-HHIA

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.32	α = 90
b = 79.25	β = 130.14
c = 67.9	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 6M		2022-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.58	55.393	99.7	0.082	0.089	0.034	16	6.6		55926

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.67			0.204	0.221	0.084	8

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	FREE R-VALUE	5YD7	1.58	55.393	55925	2909	99.576	0.149	0.1474	0.1784	11.261

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]
0.028		-0.105	0.158		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.581
r_dihedral_angle_3_deg	13.202
r_dihedral_angle_2_deg	7.682
r_dihedral_angle_1_deg	6.551
r_lrange_it	4.676
r_lrange_other	4.55
r_scangle_it	3.101
r_scangle_other	3.1
r_scbond_it	2.1
r_scbond_other	2.099
r_mcangle_it	1.782
r_mcangle_other	1.782
r_angle_refined_deg	1.735
r_mcbond_it	1.176
r_mcbond_other	1.176
r_metal_ion_refined	0.936
r_angle_other_deg	0.583
r_symmetry_nbd_refined	0.232
r_nbd_refined	0.22
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.155
r_nbd_other	0.155
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.081
r_symmetry_metal_ion_refined	0.028
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_symmetry_xyhbond_nbd_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3486
Nucleic Acid Atoms
Solvent Atoms	602
Heterogen Atoms	31

Software

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