3G0G

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	277	22.5% PEG MME 200, 0.1M Bicine pH 7.8, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.906	α = 90
b = 122.921	β = 114.77
c = 145.092	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0000	ALS	5.0.3

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	2.45	50	95.6	0.089	12.667	3.9		136864

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	2.45	2.51	78.3		0.395		2.8	7462

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3G0B	2.45	50	136813	6854	95.39	0.212	0.21	0.265	RANDOM	50.296

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]
-5.83		-0.24	7.1		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.561
r_dihedral_angle_4_deg	16.85
r_dihedral_angle_3_deg	16.302
r_dihedral_angle_1_deg	5.152
r_mcangle_it	1.953
r_scangle_it	1.596
r_angle_refined_deg	1.244
r_mcbond_it	1.212
r_scbond_it	1.075
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.561
r_dihedral_angle_4_deg	16.85
r_dihedral_angle_3_deg	16.302
r_dihedral_angle_1_deg	5.152
r_mcangle_it	1.953
r_scangle_it	1.596
r_angle_refined_deg	1.244
r_mcbond_it	1.212
r_scbond_it	1.075
r_nbtor_refined	0.312
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.142
r_symmetry_vdw_refined	0.138
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23493
Nucleic Acid Atoms
Solvent Atoms	738
Heterogen Atoms	544

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.