9IVL | pdb_00009ivl

Crystal Structure of SME-1 E166A mutant in complex with Biapenem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M lithium chloride, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.73	29.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.605	α = 90
b = 51.728	β = 90
c = 88.226	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	RIGAKU HyPix-6000HE		2023-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	22.37	99.3	0.063	0.999	18.6	6.6		40678

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	1.4	1.42			0.887

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	22.37	40618	1989	99.158	0.141	0.1388	0.1364	0.1771	0.1771	9.594

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]
-2.456			1.101		1.355

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	21.982
r_dihedral_angle_6_deg	15.917
r_dihedral_angle_2_deg	12.625
r_dihedral_angle_3_deg	11.69
r_dihedral_angle_1_deg	7.011
r_rigid_bond_restr	5.745
r_scangle_it	5.701
r_scbond_it	4.019
r_mcangle_it	3.362
r_mcbond_it	2.241
r_angle_refined_deg	2.097
r_symmetry_xyhbond_nbd_refined	0.447
r_nbtor_refined	0.315
r_symmetry_nbd_refined	0.22
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.126
r_gen_planes_refined	0.012
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2044
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	31

Software

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