9IBB | pdb_00009ibb

Rhombohedral crystalline form of human insulin complexed with m-cresol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EV3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	294.15	13.14 mg/mL human insulin, 0.80 mM zinc acetate, 0.51% v/v m-cresol in ethanol, 10.25 mM sodium thiocyanate, 0.4 M sodium-monopotassium phosphate mixture

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.684	α = 90
b = 78.684	β = 90
c = 39.883	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	PIXEL	DECTRIS EIGER X 9M		2024-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.84	39.342	99.9	0.05	0.071	0.05	0.993	5.6	1.99		7990			36.419

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.88	99.6		0.408	0.577	0.408	0.627	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.84	39.342	7988	408	99.85	0.18	0.1779	0.1781	0.2239	0.2239	46.537

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]
-0.113	-0.057		-0.113		0.368

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.045
r_dihedral_angle_6_deg	14.37
r_dihedral_angle_3_deg	13.333
r_lrange_it	8.103
r_lrange_other	8.067
r_scangle_it	6.794
r_scangle_other	6.788
r_dihedral_angle_1_deg	6.253
r_mcangle_other	5.102
r_mcangle_it	5.092
r_scbond_other	4.948
r_scbond_it	4.947
r_mcbond_it	4.289
r_mcbond_other	4.284
r_angle_refined_deg	2.134
r_angle_other_deg	0.705
r_symmetry_xyhbond_nbd_refined	0.503
r_symmetry_nbd_refined	0.217
r_nbd_other	0.212
r_nbd_refined	0.21
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.194
r_xyhbond_nbd_refined	0.184
r_ncsr_local_group_1	0.142
r_ncsr_local_group_2	0.139
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.088
r_symmetry_metal_ion_refined	0.059
r_gen_planes_refined	0.014
r_bond_refined_d	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	748
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing