6B3M | pdb_00006b3m

The crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody (70-1F02) in complex with H5 hemagglutinin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FK0	PDB entry 2FK0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.582	α = 90
b = 205.368	β = 90
c = 222.265	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	CCD	MARMOSAIC 300 mm CCD		2015-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.9	50	98.8	17.1	6.6		64141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.9

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	PDB entry 2FK0	3.92	50.01	64141	3422	93.72	0.28842	0.28626	0.2855	0.32926	0.326	RANDOM	60.359

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]
-0.03			0.53		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.658
r_dihedral_angle_3_deg	16.491
r_long_range_B_refined	15.806
r_long_range_B_other	15.806
r_dihedral_angle_4_deg	13.02
r_mcangle_it	11.501
r_mcangle_other	11.501
r_scangle_other	9.44
r_mcbond_other	6.64
r_mcbond_it	6.639
r_dihedral_angle_1_deg	6.41
r_scbond_it	5.231
r_scbond_other	5.231
r_angle_other_deg	2.475
r_angle_refined_deg	1.607
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
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	43163
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	861

Software

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