Experiment: 9MB4

Metal Beta Lactamase NDM-1 in Complex with Dual MBL/SBL Inhibitor 14

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7UP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M Lithium Sulphate,0.1M BisTris (pH 6.0),30%(v/v)Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.17	α = 90
b = 73.601	β = 89.91
c = 77.476	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	195	PIXEL	DECTRIS EIGER R 1M		2024-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	1	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.44	50	99.6	0.9804	13.65	12.93		29392

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.44	2.51			0.8654

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	7UP1	2.441	42.498	1.35	29361	2001	99.5	0.1792	0.1726	0.1751	0.2713	0.2766

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	12.217
f_angle_d	1.161
f_chiral_restr	0.059
f_bond_d	0.024
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6744
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	112

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-3000	data reduction
PHENIX	phasing