2O72 | pdb_00002o72

Crystal Structure Analysis of human E-cadherin (1-213)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EDH	PDB ENTRY 1EDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	10% PEG 8000, 0.2M calcium chloride, 5% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.341	α = 90
b = 41.077	β = 111.15
c = 59.542	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MAR scanner 345 mm plate	MIRRORS	2003-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0000	APS	19-ID

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	39.1	98	0.073	9.3	6.8	21390	20837			33

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)
	2	2.03	77.8		0.323	2.5	2.2	813

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1EDH	2	39.1	21258	20836	1068	98.02	0.226	0.193	0.191	0.2	0.234	0.24	RANDOM	19.055

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]
-0.61		-0.23	0.56		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.17
r_dihedral_angle_4_deg	19.597
r_dihedral_angle_3_deg	13.981
r_dihedral_angle_1_deg	6.414
r_scangle_it	3.347
r_scbond_it	2.262
r_angle_refined_deg	1.445
r_mcangle_it	1.323
r_mcbond_it	0.937
r_angle_other_deg	0.917
r_symmetry_vdw_other	0.221
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.204
r_mcbond_other	0.204
r_nbd_other	0.2
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.125
r_symmetry_vdw_refined	0.122
r_chiral_restr	0.089
r_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1627
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction