1WCY | pdb_00001wcy

Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Diprotin A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J2E	PDB ENTRY 1J2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	18% PEG4000, 0.18M Sodium acetate, 0.18M Gly-NaOH, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.02	α = 90
b = 126.06	β = 90
c = 136.67	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	IMAGE PLATE	RIGAKU RAXIS V			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.00	SPring-8	BL32B2

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	2.2	20	99.8	0.099	5	6.9	103739	103532			20.2

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	2.2	2.32	99.6		0.332	2.3	6.8

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1J2E	2.2	20	103739	103532	5225	99.8	0.224	0.265	RANDOM	28.8

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]
-6.67			0.3		6.38

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_angle_deg	1.25
c_improper_angle_d	0.68
c_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11990
Nucleic Acid Atoms
Solvent Atoms	1237
Heterogen Atoms	258

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNX	refinement
CCP4	data scaling
CNX	phasing