3O95 | pdb_00003o95

Crystal Structure of Human DPP4 Bound to TAK-100

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20% PEG MME 2000, 100 mM Bicine, pH 8-8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.718	α = 90
b = 123.335	β = 114.78
c = 144.419	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		2007-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1	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	2.85	50	99.3	0.106	7.7	3.3		89585

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	2.85	2.9	92.4		0.51		2.9	4581

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.85	35	90249	89524	4489	99.19	0.1901	0.187	0.2397	0.2485	0.2825	RANDOM	49.0607

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]
-2.81		-0.43	1.8		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.095
r_dihedral_angle_3_deg	18.31
r_dihedral_angle_4_deg	17.975
r_dihedral_angle_1_deg	6.404
r_scangle_it	1.527
r_angle_refined_deg	1.237
r_scbond_it	0.884
r_mcangle_it	0.629
r_mcbond_it	0.348
r_nbtor_refined	0.317
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.105
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23873
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms	510

Software

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