2ONC | pdb_00002onc

Crystal structure of human DPP-4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	20% PEG2000MME, 0.1M Bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.357	α = 90
b = 123.702	β = 114.89
c = 145.358	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	100	CCD	ADSC QUANTUM 315		2006-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		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	2.55	50	92.9	0.063	10.1	3.6		118392

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	2.55	2.63	56.6		0.389		2.7	5993

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	50	118367	5942	92.82	0.198	0.195	0.195	0.254	0.2537	RANDOM	54.148

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]
-4.33		-0.39	2.64		1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.49
r_dihedral_angle_3_deg	15.694
r_dihedral_angle_4_deg	15.647
r_dihedral_angle_1_deg	4.987
r_mcangle_it	1.66
r_scangle_it	1.399
r_angle_refined_deg	1.198
r_mcbond_it	0.993
r_scbond_it	0.887
r_nbtor_refined	0.311
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23704
Nucleic Acid Atoms
Solvent Atoms	756
Heterogen Atoms	552

Software

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