6I07

Crystal structure of EpCAM in complex with scFv

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SVZ	1SVZ, 4MZV
experimental model	PDB	4MZV	1SVZ, 4MZV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	6.4	293	0.1 M PCTP pH 6.4, 21 % w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.886	α = 90
b = 91.071	β = 90
c = 181.445	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	PIXEL	DECTRIS PILATUS3 S 6M		2015-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.35	28.7	99.2	0.061	0.999	14.7	4.8		56398			53.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.42	98		1.175	0.514	1.1	4.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1SVZ, 4MZV	2.35	28.7	53487	2851	99.2	0.23267	0.23016	0.27876	RANDOM	87.131

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]
-2.16			0.37		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.077
r_dihedral_angle_3_deg	16.06
r_dihedral_angle_4_deg	15.699
r_long_range_B_refined	12.145
r_long_range_B_other	12.144
r_mcangle_it	9.135
r_mcangle_other	9.134
r_scangle_other	8.279
r_dihedral_angle_1_deg	7.975
r_mcbond_it	5.928
r_mcbond_other	5.927
r_scbond_it	5.28
r_scbond_other	5.28
r_angle_refined_deg	1.418
r_angle_other_deg	1.183
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7118
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	6

Software

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