3W80 | pdb_00003w80

Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W7Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.67	293	10mg/ml protein, 0.1M Sodium Citrate, 22%(v/v) DMF, 0.08%(w/v) Zinc chloride, pH 8.67, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.72	α = 90
b = 82.72	β = 90
c = 68.14	γ = 120

Symmetry
Space Group	H 3

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	Fully automatic high speed Weissenberg data collection system called Galaxy	The vertically focusing 1m long bent mirror of Pt-coated fused silica is 21m from the SR source point and 7m from the focus point	2003-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6C	1.00	Photon Factory	BL-6C

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	1	50		0.05476		4.46		90240

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	3w7y	1.4	10	32370	1700	99.46	0.18539	0.1822	0.18	0.24845	0.25	RANDOM	24.619

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]
0.05	0.05		0.05		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	49.868
r_dihedral_angle_2_deg	35.54
r_sphericity_bonded	22.922
r_dihedral_angle_3_deg	11.746
r_dihedral_angle_4_deg	6.368
r_dihedral_angle_1_deg	5.562
r_rigid_bond_restr	2.889
r_angle_refined_deg	1.258
r_chiral_restr	0.082
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	49.868
r_dihedral_angle_2_deg	35.54
r_sphericity_bonded	22.922
r_dihedral_angle_3_deg	11.746
r_dihedral_angle_4_deg	6.368
r_dihedral_angle_1_deg	5.562
r_rigid_bond_restr	2.889
r_angle_refined_deg	1.258
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1620
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	4

Software

Software
Software Name	Purpose
WEIS	data scaling
CCP4	model building
REFMAC	refinement
WEIS	data reduction
CCP4	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.