3WQH | pdb_00003wqh

Crystal Structure of human DPP-IV in complex with Anagliptin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BJM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	18% PEG 4000, 15% PEG 1000, 0.15M Na/K-Phosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.16	α = 90
b = 68.99	β = 90
c = 419.6	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2013-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU		SPring-8	BL41XU

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	49.11	99.9	0.149	12.1			45509

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.92	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	3BJM	2.85	47.67	45508	2275	100	0.227	0.22	0.288	0.22	RANDOM	54.87

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]

RMS Deviations
Key	Refinement Restraint Deviation
o_angle_deg	1.85327
o_improper_angle_d	0.37595
o_bond_d	0.01196
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11926
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	239

Software

Software
Software Name	Purpose
XDS	data scaling
MOLREP	phasing
PRIME-X	refinement
XDS	data reduction
XSCALE	data scaling