Experiment: 9GX8

Crystal structure of CIM-2, a membrane-bound B1 metallo-beta-lactamase from Chryseobacterium indologenes

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292.15	0.1M Tris/Bicine pH8.5, 0.12 M (1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol), 37.5% (MPD, PEG1000, Peg3350)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.287	α = 90
b = 43.131	β = 115.959
c = 75.691	γ = 90

Symmetry
Space Group	C 1 2 1

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		2024-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.27021	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.56	73.86	99.2	0.044	0.998	12	6.7		67879			23.51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.59	96.5		1.053	0.283	0.5

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	SAD	FREE R-VALUE	1.56	41.76	1.33	67580	1941	98.72	0.1687	0.168	0.1705	0.1946	0.1972	30.14

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	23.9726
f_angle_d	0.7832
f_chiral_restr	0.0562
f_bond_d	0.0057
f_plane_restr	0.0044

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3526
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	35

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
CRANK2	phasing