8B20 | pdb_00008b20

NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP57

X-RAY DIFFRACTION

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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 hexahydrate, 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	37.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.068	α = 90
b = 70.444	β = 90
c = 73.803	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	1.78	53.31	100	0.178	6.8	7.1		39230

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	1.78	1.82	100		0.956	2.1	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6TGD	1.78	53.306	39169	1900	99.931	0.185	0.184	0.19	0.2073	0.21	RANDOM	26

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]
0.603			1.418		-2.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.708
r_dihedral_angle_4_deg	21.34
r_dihedral_angle_3_deg	13.673
r_dihedral_angle_1_deg	6.777
r_lrange_it	6.145
r_scangle_it	4.862
r_scbond_it	3.278
r_mcangle_it	3.065
r_mcbond_it	2.182
r_angle_refined_deg	1.574
r_symmetry_nbd_refined	0.328
r_nbtor_refined	0.318
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.114
r_chiral_restr	0.105
r_gen_planes_refined	0.01
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	61

Software

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