8QNZ

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	HEPES pH 7.5 no Cl-, 11.6% PEG8000, 8% 1-BuOH mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.31	α = 90
b = 105.965	β = 90
c = 124.679	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 X 16M		2020-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.918381	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.53	80.74	98.3	0.999	12	13.6		159414

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.56			0.62	1.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.53	62.417	159336	7990	98.133	0.149	0.1463	0.1988	21.078

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]
2.363			-0.705		-1.659

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.462
r_dihedral_angle_4_deg	15.495
r_dihedral_angle_3_deg	12.638
r_dihedral_angle_1_deg	6.012
r_lrange_it	3.4
r_scangle_it	3.202
r_scangle_other	3.201
r_lrange_other	3.196
r_scbond_it	2.765
r_scbond_other	2.765
r_mcangle_it	2.252
r_mcangle_other	2.252
r_rigid_bond_restr	1.982
r_mcbond_it	1.859
r_mcbond_other	1.85
r_angle_refined_deg	1.474
r_angle_other_deg	1.443
r_symmetry_nbd_refined	0.293
r_nbd_refined	0.239
r_nbd_other	0.198
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8012
Nucleic Acid Atoms
Solvent Atoms	1019
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing