5WIB | pdb_00005wib

Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K0X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	298	100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.398	α = 90
b = 144.744	β = 90
c = 43.95	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 225 mm CCD		2015-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.868	81.38	100	0.051	0.999	18.7	6		53055

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.868	1.875	100		0.866	0.781	1.9	6.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4K0X	1.87	81.38	50364	2613	99.83	0.18792	0.18582	0.2	0.22843	0.24	RANDOM	47.631

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]
0.88			0.32		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.81
r_dihedral_angle_3_deg	13.629
r_dihedral_angle_4_deg	10.623
r_dihedral_angle_1_deg	7.837
r_long_range_B_refined	7.614
r_long_range_B_other	7.54
r_scangle_other	5.379
r_mcangle_it	4.059
r_mcangle_other	4.058
r_scbond_other	3.794
r_scbond_it	3.793
r_mcbond_it	3.017
r_mcbond_other	3.017
r_angle_refined_deg	1.231
r_angle_other_deg	0.664
r_chiral_restr	0.088
r_gen_planes_refined	0.02
r_bond_refined_d	0.009
r_gen_planes_other	0.003
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3743
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	35

Software

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