9CIV | pdb_00009civ

X-Ray Structure of Insulin Analog DETEMIR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.2M Lithium sulfate monohydrate, 0.1M Tris pH 8.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.698	α = 90
b = 78.698	β = 90
c = 39.825	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 PILATUS 6M		2023-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.6	39.35	95.3	0.032	0.034	0.02	12.6	3		11559

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	8.76	39.35			0.024	0.032	0.021

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	THROUGHOUT	1.6	39.349	11557	1173	95.229	0.199	0.1932	0.1848	0.2483	0.24	46.086

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]
-0.554	-0.277		-0.554		1.798

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.607
r_dihedral_angle_3_deg	14.064
r_lrange_other	13.225
r_lrange_it	13.216
r_scangle_it	11.274
r_scangle_other	11.265
r_scbond_it	8.06
r_scbond_other	8.053
r_mcangle_other	7.756
r_mcangle_it	7.733
r_dihedral_angle_1_deg	6.9
r_mcbond_it	6.09
r_mcbond_other	6.079
r_dihedral_angle_other_2_deg	3.075
r_angle_refined_deg	2.176
r_dihedral_angle_2_deg	2.11
r_angle_other_deg	0.738
r_nbd_refined	0.226
r_nbtor_refined	0.212
r_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.207
r_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.189
r_symmetry_nbd_refined	0.131
r_chiral_restr	0.103
r_metal_ion_refined	0.096
r_symmetry_metal_ion_refined	0.096
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	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	794
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
TRUNCATE	data reduction
MOLREP	phasing