Experiment: 8HY6

Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	4RL0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M Bis-Tris (PH 6.0), 0.2 M Lithium sulfate, 25%-37% (v/v) Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.313	α = 90
b = 79.301	β = 90
c = 133.698	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	195	PIXEL	DECTRIS PILATUS3 X CdTe 1M		2019-11-03	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)	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	1.4	50	99.5	0.059	13.4	12		82934

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	1.4	1.42	96.7		0.37		9.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	1.4	30.8	1.35	82810	1999	99.47	0.143	0.1425	0.1565	0.1643	0.182

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	17.351
f_angle_d	1.056
f_chiral_restr	0.082
f_bond_d	0.012
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3594
Nucleic Acid Atoms
Solvent Atoms	448
Heterogen Atoms	62

Software

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