3CCC

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	277	22.5% PEG 2000mme, 0.1M Bicine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.899	α = 90
b = 121.958	β = 114.94
c = 144.275	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		CCD	ADSC		2004-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	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	2.75	50	92.5	0.074	10.2	2.2		94607

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	2.85	90.1		0.567		2	9212

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.71	46.13	94570	4722	90.88	0.204	0.2	0.267	RANDOM	58.239

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]
-0.22			0.14		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.495
r_dihedral_angle_4_deg	17.395
r_dihedral_angle_3_deg	16.961
r_dihedral_angle_1_deg	5.251
r_mcangle_it	1.824
r_scangle_it	1.436
r_angle_refined_deg	1.263
r_mcbond_it	1.102
r_scbond_it	0.936
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23716
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	364

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction