3JYH | pdb_00003jyh

Human dipeptidyl peptidase DPP7

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	300	2M Ammonium sulfate, 0.2M Sodium acetate, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.216	α = 90
b = 130.215	β = 102.36
c = 124.436	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		2009-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.19	100	100	0.111	25.9	9.8		127772

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	2.19	2.22	99.9

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	2.19	100	127511	6400	98.85	0.182	0.18	0.1805	0.222	0.2231	RANDOM	33.22

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]
0.96		-1.43	-1.36		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.572
r_dihedral_angle_4_deg	18.862
r_dihedral_angle_3_deg	13.188
r_dihedral_angle_1_deg	5.86
r_scangle_it	2.904
r_scbond_it	1.875
r_angle_refined_deg	1.346
r_mcangle_it	1.271
r_mcbond_it	0.732
r_nbtor_refined	0.31
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13852
Nucleic Acid Atoms
Solvent Atoms	946
Heterogen Atoms	341

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
HKL-3000	data scaling