3O9V

Crystal Structure of Human DPP4 Bound to TAK-986

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9M	pdb entry 1R9M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop, vapor diffusion		277	20% PEG MME 2000, 100 mM Bicine, pH 8-8.5, sitting drop, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.166	α = 90
b = 122.886	β = 114.59
c = 144.909	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	92	CCD	ADSC QUANTUM 315r		2007-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

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	2.75	50	98.9	0.087	9.6	3.2	101631	100525

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	2.75	2.8	98.6		0.514		2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 1R9M	2.75	35	101701	95320	5026	98.65	0.20619	0.20338	0.25	0.25961	0.29	RANDOM	41.346

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]
-1.08		0.04	0.97		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.267
r_dihedral_angle_3_deg	17.821
r_dihedral_angle_4_deg	17.155
r_dihedral_angle_1_deg	6.349
r_scangle_it	1.495
r_angle_refined_deg	1.222
r_scbond_it	0.925
r_angle_other_deg	0.875
r_mcangle_it	0.684
r_mcbond_it	0.397
r_symmetry_vdw_other	0.27
r_nbd_other	0.203
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.19
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_other	0.1
r_nbtor_other	0.095
r_chiral_restr	0.072
r_mcbond_other	0.061
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23879
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	372

Software

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