1R9N

Crystal Structure of human dipeptidyl peptidase IV in complex with a decapeptide (tNPY) at 2.3 Ang. Resolution

X-RAY DIFFRACTION

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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	VAPOR DIFFUSION, SITTING DROP	8.25	298	PEG 2000, Bicine, pH 8.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.606	α = 90
b = 122.701	β = 114.88
c = 145.405	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	173	CCD	ADSC QUANTUM 4		2003-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.01	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	23270		0.075	0.054	11.7	2	161260	161260	1	1

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	2.3	2.36	94.2		0.429	1.8	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry: 1R9M	2.3	41.17	161260	153134	8078	100	0.2127	0.21065	0.2514	RANDOM	47.6

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]
-3.14		-1.17	3.08		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.607
r_dihedral_angle_4_deg	18.533
r_dihedral_angle_3_deg	17.555
r_dihedral_angle_1_deg	6.406
r_scangle_it	1.708
r_angle_refined_deg	1.276
r_scbond_it	1.09
r_mcangle_it	0.769
r_mcbond_it	0.445
r_nbtor_refined	0.308
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24028
Nucleic Acid Atoms
Solvent Atoms	1249
Heterogen Atoms	350

Software

Software
Software Name	Purpose
REFMAC	refinement
CCP4	data scaling
AMoRE	phasing