2YBR | pdb_00002ybr

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CN2	HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB
experimental model	PDB	1QLR	HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB
experimental model	PDB	1DFB	HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.

Crystal Properties
Matthews coefficient	Solvent content
2.61	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.844	α = 90
b = 104.494	β = 90
c = 152.55	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	110	CCD	MARRESEARCH MX-300	MIRRORS	2009-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G		APS	21-ID-G

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	2.55	46.2	99.9	0.1	6.4	6.4		37179		2	32.8

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	2.55	2.69	100		0.33	2.3	6.5

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	HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB	2.55	45.72	35277	1858	99.9	0.19455	0.19183	0.19	0.24673	0.24	RANDOM	32.766

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]
-1.02			0.63		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.901
r_dihedral_angle_4_deg	22.144
r_dihedral_angle_3_deg	14.996
r_scangle_it	7.155
r_dihedral_angle_1_deg	5.856
r_scbond_it	5.184
r_mcangle_it	4.702
r_mcbond_it	3.344
r_angle_refined_deg	1.257
r_chiral_restr	0.078
r_bond_refined_d	0.009
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_other
r_mcangle_other
r_scbond_other
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	6721
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms

Software

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