7PSE

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Oxacillin

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
2.44	49.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.83	α = 90
b = 105.48	β = 90
c = 124.96	γ = 90

Symmetry
Space Group	P 2 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		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976270	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	2.32	53.76	99.3	0.996	7	10.9		26329

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	2.32	2.4			0.566	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	2.32	53.76	26280	1266	99.215	0.238	0.2352	0.2886	46.938

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]
4.801			-0.452		-4.349

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.754
r_dihedral_angle_3_deg	16.295
r_dihedral_angle_4_deg	14.331
r_lrange_it	8.528
r_lrange_other	8.528
r_dihedral_angle_1_deg	7.153
r_mcangle_it	6.128
r_mcangle_other	6.128
r_scangle_it	5.765
r_scangle_other	5.764
r_mcbond_other	3.957
r_mcbond_it	3.956
r_scbond_it	3.614
r_scbond_other	3.613
r_angle_refined_deg	1.529
r_angle_other_deg	1.195
r_nbd_refined	0.214
r_nbd_other	0.189
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.128
r_chiral_restr_other	0.125
r_symmetry_nbd_refined	0.122
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.074
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3958
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	77

Software

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