2OMG | pdb_00002omg

Structure of human insulin cocrystallized with protamine and urea

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7INS	insulin trimer R-conformation

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	291	60mM m-cresol, 3M urea, 1.0 mg/ml protamine sulphate, 400mM NaCl, 40mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.66	α = 90
b = 61.66	β = 90
c = 85.54	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2004-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-5	0.969	MAX II	I911-5

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	1.52	50	93	0.082	14.4	8	27022	25119			30.5

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	1.52	1.6	74.7		0.33	4.9	6	4630

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	insulin trimer R-conformation	1.52	25.88	23837	1276	95.99	0.18391	0.18253	0.1937	0.20947	0.2206	RANDOM	28.01

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.987
r_dihedral_angle_3_deg	11.45
r_dihedral_angle_4_deg	8.404
r_dihedral_angle_1_deg	6.769
r_scangle_it	4.054
r_scbond_it	2.61
r_mcangle_it	1.667
r_angle_refined_deg	1.545
r_angle_other_deg	0.945
r_mcbond_it	0.935
r_symmetry_vdw_refined	0.334
r_symmetry_hbond_refined	0.305
r_xyhbond_nbd_refined	0.294
r_nbd_refined	0.289
r_mcbond_other	0.287
r_nbtor_refined	0.205
r_nbd_other	0.195
r_symmetry_vdw_other	0.187
r_metal_ion_refined	0.184
r_chiral_restr	0.103
r_nbtor_other	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1163
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing