9JNF | pdb_00009jnf

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

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	20% PEG 4000, 0.2 M Lithium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.02	37.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.112	α = 90
b = 50.672	β = 92.521
c = 130.339	γ = 90

Symmetry
Space Group	P 1 21 1

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		2024-07-23	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)	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	23.952	99.9	0.994	11.8	5.6		20650

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			0.929

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	2.32	23.952	20634	1043	99.807	0.188	0.1833	0.1836	0.2802	0.2814	19.207

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]
-0.797		-1.313	-0.51		1.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.932
r_dihedral_angle_6_deg	14.155
r_dihedral_angle_2_deg	13.054
r_lrange_it	9.642
r_dihedral_angle_1_deg	8
r_scangle_it	4.924
r_rigid_bond_restr	4.193
r_mcangle_it	3.896
r_scbond_it	3.162
r_angle_refined_deg	2.579
r_mcbond_it	2.418
r_symmetry_nbd_refined	0.36
r_nbtor_refined	0.317
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.194
r_chiral_restr	0.172
r_ncsr_local_group_1	0.109
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4108
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	85

Software

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