7PEI

Crystal Structure of a Class D carbapenemase_E185A/R186A/R206A

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	6.8	291	0.2M LiSO4, 21% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.186	α = 90
b = 146.186	β = 90
c = 54.887	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979150	SSRF	BL17U1

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	1.9	19.69	99.9	0.999	16.1	20.6		52999

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	1.9	1.94			0.726	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	1.9	19.69	52978	2657	99.855	0.179	0.1773	0.2112	38.061

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]
-2.323	-1.161		-2.323		7.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.88
r_dihedral_angle_4_deg	22.021
r_dihedral_angle_3_deg	14.327
r_lrange_it	7.076
r_lrange_other	7.019
r_scangle_it	6.096
r_scangle_other	6.068
r_dihedral_angle_1_deg	5.954
r_scbond_it	4.012
r_mcangle_it	3.986
r_mcangle_other	3.986
r_scbond_other	3.965
r_mcbond_it	2.912
r_mcbond_other	2.897
r_angle_refined_deg	1.583
r_angle_other_deg	1.299
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.18
r_symmetry_nbd_other	0.167
r_nbtor_refined	0.159
r_nbd_other	0.153
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.074
r_symmetry_nbd_refined	0.069
r_ncsr_local_group_1	0.069
r_symmetry_xyhbond_nbd_other	0.014
r_bond_refined_d	0.009
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	3934
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing