9TB1 | pdb_00009tb1

Crystal structure of an acylated GLP-1/GIP analogue peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1M sodium citrate pH 4.5, 0.2M ammonium phosphate monobasic, 0.1M ammonium sulfate, 32% v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.95	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.66	α = 90
b = 64.66	β = 90
c = 11.417	γ = 90

Symmetry
Space Group	P 43

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 EIGER2 S 9M		2024-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.62	Diamond	I24

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	1.59	64.66	99.8	0.269	0.318	0.169	0.988	3.8	6.3		6855

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)
	1.59	1.62	100		2.936	3.48	1.85	0.173	0.7	6.3

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	1.59	64.66	6852	674	99.767	0.212	0.2083	0.2163	0.245	0.2562	24.604

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]
-1.187			-1.187		2.373

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.065
r_lrange_other	17.74
r_dihedral_angle_3_deg	15.141
r_dihedral_angle_6_deg	13.807
r_scangle_it	10.577
r_scangle_other	10.554
r_mcangle_other	9.335
r_mcangle_it	9.279
r_scbond_it	7.351
r_scbond_other	7.329
r_rigid_bond_restr	6.172
r_mcbond_it	6.069
r_mcbond_other	5.903
r_dihedral_angle_1_deg	5.681
r_angle_refined_deg	2.05
r_angle_other_deg	0.776
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.218
r_nbtor_refined	0.197
r_nbd_other	0.16
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_other	0.155
r_symmetry_xyhbond_nbd_refined	0.148
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	255
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DIALS	data reduction
xia2	data reduction
Aimless	data scaling
MrBUMP	phasing
BUCCANEER	model building
Coot	model building
REFMAC	refinement