4U6H | pdb_00004u6h

Vaccinia L1/M12B9-Fab complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YPY	1YPY,1SY6
experimental model	PDB	1SY6	1YPY,1SY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Initial crystallization experiments were carried out by sitting-drop vapor diffusion in a 96-well format, using a Phoenix liquid-handling robot with a panel of commercial sparse-matrix screens (PEG/Ion 1 and 2 from Hampton Research, Wizard 2 from Emerald Biosciences, JCSG Plus Suite from Qiagen, and JBScreen 6 from Jena BioScience). Quality diffracting crystals of L1/M12B9-Fab complex were obtained at RT by mixing 0.5ul of protein solution at 9.5 mg/ml with 0.5ul of precipitant [100 mM Tris, pH 7.0, 20% (w/v) polyethylene glycol (PEG) 3000, and 200 mM Ca(OAc)] and seeding with initial crystals obtained at 6.5 mg/ml. Crystal were flash-frozen at 100K in mother liquor containing 20 % glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.829	α = 90
b = 102.829	β = 90
c = 238.355	γ = 120

Symmetry
Space Group	P 32 2 1

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		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	3.1	47.67	99.9	0.2	0.077	9.7	9.2		27308		1.7

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	FREE R-VALUE	1YPY,1SY6	3.1	47.21	25898	1367	99.9	0.21221	0.20938	0.21	0.26491	0.27	RANDOM	64.52

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.017
r_dihedral_angle_4_deg	14.581
r_dihedral_angle_3_deg	12.955
r_dihedral_angle_1_deg	4.964
r_angle_refined_deg	0.865
r_angle_other_deg	0.644
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	9188
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement