Experiment: 4IOF

Crystal structure analysis of Fab-bound human Insulin Degrading Enzyme (IDE)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CWW	PDB ENTRY 3CWW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	0.1M Sodium cacodylate, pH6.5; 0.2M MgCl2; 10% PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.955	α = 90
b = 131.662	β = 90
c = 377.039	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	278	CCD	ADSC QUANTUM 315		2012-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	3.353	50	99.9	0.119	0.119	14.1	5.6	41849	40227	3.2	3.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.353	3.42	100		0.688	0.688	3.2	5.6

Refinement

Statistics
Diffraction ID	Structure Solution 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	PDB ENTRY 3CWW	3.353	49.852	41849	40227	2010	99.9	0.2346	0.2346	0.2322	0.2349	0.2803	0.2767	Random

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.731
f_angle_d	1.578
f_chiral_restr	0.105
f_plane_restr	0.008
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20937
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling