4LQF | pdb_00004lqf

Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at the resolution of 2.3 Angstroms

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HDI	A20G2-Fv domain (reported in same publication), conserved domain of 3E5 IgG3 Fab (extracted from pdb entry 4HDI), one monomer of A33 (extracted from pdb entry 3K7B)
experimental model	PDB	3K7B	A20G2-Fv domain (reported in same publication), conserved domain of 3E5 IgG3 Fab (extracted from pdb entry 4HDI), one monomer of A33 (extracted from pdb entry 3K7B)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	20% PEG3000, 0.1M imidazole, 0.2M zinc acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.28	α = 90
b = 73.18	β = 90
c = 221.6	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS 6M	Monochromator Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs, Crystal Type Si(111), Mirrors Rh coated flat mirror	2013-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	49.76	96.9	0.095	0.095	11.3	4.8	26224	25343		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	90.9		0.644	0.644	2	4.4

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	A20G2-Fv domain (reported in same publication), conserved domain of 3E5 IgG3 Fab (extracted from pdb entry 4HDI), one monomer of A33 (extracted from pdb entry 3K7B)	2.3	49.76	23980	1283	96.32	0.19897	0.1973	0.19	0.23046	0.23	RANDOM	34.391

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]
1.51			-1.75		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.075
r_dihedral_angle_4_deg	17.184
r_dihedral_angle_3_deg	13.393
r_dihedral_angle_1_deg	5.884
r_angle_refined_deg	1.006
r_chiral_restr	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3905
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	4

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	data scaling