7PEP

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem

X-RAY DIFFRACTION

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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
2.33	47.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.946	α = 90
b = 107.93	β = 90
c = 124.42	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	1.7	69.685	100	0.999	9.8	13.3		124585

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	1.7	1.73			0.706	1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4S2P	1.7	69.685	124488	6286	99.937	0.2	0.1986	0.2306	23.851

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]
3.209			-0.405		-2.804

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.64
r_dihedral_angle_4_deg	14.909
r_dihedral_angle_3_deg	13.152
r_dihedral_angle_1_deg	6.018
r_lrange_it	5.251
r_lrange_other	5.115
r_scangle_it	3.831
r_scangle_other	3.831
r_mcangle_it	2.547
r_mcangle_other	2.547
r_scbond_it	2.477
r_scbond_other	2.477
r_mcbond_it	1.752
r_mcbond_other	1.75
r_angle_refined_deg	1.518
r_angle_other_deg	1.369
r_nbd_refined	0.221
r_nbd_other	0.203
r_symmetry_nbd_refined	0.181
r_symmetry_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.164
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.074
r_ncsr_local_group_3	0.068
r_ncsr_local_group_5	0.068
r_ncsr_local_group_4	0.065
r_ncsr_local_group_2	0.063
r_ncsr_local_group_6	0.06
r_ncsr_local_group_1	0.059
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	7989
Nucleic Acid Atoms
Solvent Atoms	878
Heterogen Atoms	100

Software

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