Experiment: 8B1W

NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP35

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TGD	6TGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 exahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.19	α = 90
b = 73.699	β = 90
c = 77.28	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 EIGER2 XE 16M		2022-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.873	ESRF	ID23-1

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	1.7	36.88	99.7	0.194	8.6	5.4		44671

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	1.7	1.73	99.5		0.531		4.4

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	6TGD	1.7	36.88	44139	2185	98.52	0.193	0.1915	0.1916	0.2224	0.2224	RANDOM	22

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]
0.03			0.02		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.209
r_dihedral_angle_4_deg	21.337
r_dihedral_angle_3_deg	13.754
r_dihedral_angle_1_deg	6.842
r_angle_refined_deg	1.568
r_chiral_restr	0.106
r_gen_planes_refined	0.01
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing