4KPH | pdb_00004kph

Structure of the Fab fragment of N62, a protective monoclonal antibody to the nonreducing end of Francisella tularensis O-antigen

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OZ9	pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain)
experimental model	PDB	3D9A	pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	Microseeding by mixing 0.5 ul of Fab (12 mg/ml in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.02% NaN3) with 0.5 ul of reservoir solution [0.1 M bistris (pH 6.5), 0.2 M ammonium acetate, 25% w/v PEG 3350] and streaking after equilibration, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.874	α = 90
b = 87.076	β = 90
c = 153.589	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2012-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.593	15	98.8	0.068	14.6	3.8		28828		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	98.1		0.325		3.7

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain)	2.59	14.87	28036	1946	96	0.225	0.222	0.22	0.268	0.27	36.78

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.369
f_angle_d	0.666
f_chiral_restr	0.043
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6220
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.