2WBY | pdb_00002wby

Crystal structure of human insulin-degrading enzyme in complex with insulin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G47	PDB ENTRY 2G47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE

Crystal Properties
Matthews coefficient	Solvent content
3.8	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 262.319	α = 90
b = 262.319	β = 90
c = 90.609	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	287	CCD			2007-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	2.6	50	99.9	0.13	21	7		109017		1

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	2.6	2.69	100		0.52	4.8	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	PDB ENTRY 2G47	2.6	32.08	103440	5438	99.9	0.167	0.164	0.17	0.218	0.22	RANDOM	28.81

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.324
r_dihedral_angle_4_deg	22.892
r_dihedral_angle_3_deg	20.115
r_dihedral_angle_1_deg	6.809
r_scangle_it	5.42
r_scbond_it	3.421
r_angle_refined_deg	2.101
r_mcangle_it	1.881
r_mcbond_it	1.115
r_nbtor_refined	0.325
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.24
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.139
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	16202
Nucleic Acid Atoms
Solvent Atoms	722
Heterogen Atoms	2

Software

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