5WI7

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

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
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.017	α = 90
b = 143.895	β = 90
c = 44.563	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	1.861	81.57	99.9	0.102	0.994	10.2	6.1		54365

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	1.861	1.867	99.5		0.784	0.767	2.1	6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4K0X	1.861	30	51671	2642	99.79	0.20045	0.1995	0.21839	RANDOM	39.356

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]
0.92			-1.3		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.071
r_dihedral_angle_3_deg	12.867
r_dihedral_angle_4_deg	9.307
r_long_range_B_other	6.047
r_long_range_B_refined	6.041
r_dihedral_angle_1_deg	5.278
r_scangle_other	2.959
r_mcangle_it	2.499
r_mcangle_other	2.498
r_scbond_other	1.806
r_scbond_it	1.805
r_mcbond_it	1.521
r_mcbond_other	1.52
r_angle_refined_deg	1.347
r_angle_other_deg	0.901
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	3736
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	48

Software

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