8GRT

Small Dipeptide Analogues developed by Co-crystal Structure of Stenotrophomonas maltophilia Dipeptidyl Peptidase 7

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	20% PEG 8000, 200mM Amm. Acetate, 20% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.2	α = 90
b = 74.25	β = 95.11
c = 154.59	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	RAYONIX MX-300		2016-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.59	34.58	99	0.109	0.128	0.066	0.994	10.4	3.7		47008			35.788

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.63	84.8		0.565	0.361	0.727		2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7DKB	2.59	30.002	46981	2287	98.895	0.179	0.1754	0.2429	Random selection	40.889

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]
0.587		-0.075	0.246		-0.807

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.255
r_dihedral_angle_6_deg	14.913
r_dihedral_angle_1_deg	7.314
r_lrange_it	7.095
r_lrange_other	7.094
r_dihedral_angle_2_deg	6.014
r_scangle_it	5.3
r_scangle_other	5.299
r_mcangle_it	4.628
r_mcangle_other	4.628
r_scbond_it	3.381
r_scbond_other	3.381
r_mcbond_it	3.007
r_mcbond_other	3.007
r_chiral_restr_other	1.434
r_angle_refined_deg	1.413
r_angle_other_deg	0.535
r_symmetry_xyhbond_nbd_refined	0.302
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.215
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.156
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.061
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10701
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
xia2	data reduction
DIALS	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building
BUCCANEER	model building
PHENIX	model building