2NTF

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A6V	PDB ENTRIES 1A6V, 1MFB
experimental model	PDB	1MFB	PDB ENTRIES 1A6V, 1MFB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	298	1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.659	α = 90
b = 118.659	β = 90
c = 176.042	γ = 90

Symmetry
Space Group	P 43 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 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY	2006-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	3.18	50	88.6	0.096	14.2	2.2		19140			77.3

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	3.18	3.25	95		0.508	2	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 ENTRIES 1A6V, 1MFB	3.18	44.02	18770	18458	992	89.1	0.213	0.21	0.265	RANDOM	63.65

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]
1.27			1.27		-2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.955
r_dihedral_angle_3_deg	18.045
r_dihedral_angle_4_deg	16.975
r_dihedral_angle_1_deg	8.267
r_scangle_it	2.296
r_scbond_it	1.662
r_angle_refined_deg	1.549
r_mcangle_it	1.107
r_mcbond_it	0.927
r_angle_other_deg	0.894
r_symmetry_vdw_other	0.414
r_symmetry_hbond_refined	0.331
r_symmetry_vdw_refined	0.305
r_nbd_refined	0.23
r_nbd_other	0.21
r_nbtor_refined	0.199
r_xyhbond_nbd_refined	0.15
r_mcbond_other	0.135
r_nbtor_other	0.096
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6610
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing