3DW0

Crystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	20% PEG 6000, 0.1 M KSCN, 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.3	α = 90
b = 91.3	β = 112.6
c = 73.1	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	77	IMAGE PLATE	MAR scanner 345 mm plate	mirror 1, double crystal, mirror 2	2006-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97900	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.6	19.76	96.5	0.05	21.54	3.3		86680			14.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.7	95.2		0.137	11.68	3	14100

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	PDB entry 1DY6	1.6	19.76	82347	4335	100	0.18875	0.18758	0.2108	RANDOM	10.889

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]
-0.02		-0.22	0.36		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.886
r_dihedral_angle_4_deg	15.125
r_dihedral_angle_3_deg	11.953
r_dihedral_angle_1_deg	5.478
r_sphericity_free	4.654
r_scangle_it	3.059
r_sphericity_bonded	2.353
r_scbond_it	2.125
r_mcangle_it	1.375
r_angle_refined_deg	1.255
r_rigid_bond_restr	1.185
r_mcbond_it	0.936
r_nbtor_refined	0.304
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.084
r_symmetry_hbond_refined	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3953
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Xnemo	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing