3E4Z | pdb_00003e4z

Crystal structure of human insulin degrading enzyme in complex with insulin-like growth factor II

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	10-13% PEG MME 5000, 100 mM HEPES pH 7.0, 4-14% Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 263.033	α = 90
b = 263.033	β = 90
c = 90.816	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MAR scanner 345 mm plate		2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		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	2.28	50	99.9	0.134	0.105	20.1	5.4	162414	162414	1	1	13.4

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)
	2.28	2.36	99.9		0.507	0.539	2.1	3.1	15661

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.28	50	162414	154214	8139	99.71	0.19746	0.19577	0.21	0.22983	0.24	RANDOM	36.385

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]
-0.27	-0.14		-0.27		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	17.664
r_dihedral_angle_1_deg	5.859
r_scangle_it	3.163
r_scbond_it	1.957
r_angle_refined_deg	1.336
r_mcangle_it	1.153
r_mcbond_it	0.695
r_symmetry_hbond_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	21.843
r_dihedral_angle_3_deg	17.664
r_dihedral_angle_1_deg	5.859
r_scangle_it	3.163
r_scbond_it	1.957
r_angle_refined_deg	1.336
r_mcangle_it	1.153
r_mcbond_it	0.695
r_symmetry_hbond_refined	0.311
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15685
Nucleic Acid Atoms
Solvent Atoms	724
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASES	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.