7A3G

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, 91

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		273	0.46 M Na citrate

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.598	α = 90
b = 153.598	β = 90
c = 270.222	γ = 120

Symmetry
Space Group	P 61

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 X 16M		2020-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.8	49.43	100	0.091	0.095	0.999	19.17	13.177		88413			78.124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	100		1.546	1.606	0.792	2.04	13.645

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	6EOP	2.8	49.43	83992	4421	99.97	0.2107	0.209	0.2423	RANDOM	89.573

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]
2.07	1.03		2.07		-6.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.629
r_dihedral_angle_3_deg	14.126
r_dihedral_angle_4_deg	13.966
r_dihedral_angle_1_deg	6.085
r_angle_refined_deg	1.365
r_angle_other_deg	0.866
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.629
r_dihedral_angle_3_deg	14.126
r_dihedral_angle_4_deg	13.966
r_dihedral_angle_1_deg	6.085
r_angle_refined_deg	1.365
r_angle_other_deg	0.866
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13435
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	206

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.