7PEH

Crystal Structure of a Class D Carbapenemase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4S2P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.003	α = 90
b = 106.976	β = 90
c = 124.611	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 EIGER X 16M		2021-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.815342	Diamond	I03

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	1.92	53.84	99.9	0.994	5.8	12		85231

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	1.92	1.96			0.588	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	1.92	53.84	85147	4389	99.862	0.22	0.2184	0.2495	24.047

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]
3.04			-0.748		-2.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.889
r_dihedral_angle_4_deg	14.962
r_dihedral_angle_3_deg	13.8
r_dihedral_angle_1_deg	6.325
r_lrange_it	4.26
r_lrange_other	4.214
r_scangle_it	3.312
r_scangle_other	3.312
r_mcangle_it	2.375
r_mcangle_other	2.375
r_scbond_it	2.119
r_scbond_other	2.119
r_mcbond_it	1.559
r_mcbond_other	1.559
r_angle_refined_deg	1.415
r_angle_other_deg	1.288
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.214
r_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.168
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.069
r_ncsr_local_group_4	0.065
r_ncsr_local_group_5	0.064
r_ncsr_local_group_2	0.062
r_ncsr_local_group_3	0.06
r_ncsr_local_group_6	0.054
r_ncsr_local_group_1	0.047
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7932
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	35

Software

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