6IBV

Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic inhibitor cpd 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.407	α = 90
b = 73.824	β = 90
c = 77.868	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.4	42.63	99.66	0.074	0.036	0.991	9.94	9.1		80341

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	99.34		0.543	0.622	0.298	0.956	2.77	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.4	42.67	76006	4263	99.72	0.21964	0.21778	0.25205	RANDOM	15.475

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]
-1.8			3.32		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.29
r_dihedral_angle_4_deg	20.741
r_dihedral_angle_3_deg	13.451
r_dihedral_angle_1_deg	7.06
r_long_range_B_refined	5.817
r_scbond_it	2.53
r_mcangle_it	2.085
r_angle_refined_deg	1.906
r_mcbond_it	1.328
r_chiral_restr	0.147
r_gen_planes_refined	0.012
r_bond_refined_d	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3382
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing