7DKC

Stenotrophomonas maltophilia DPP7 in complex with Tyr-Tyr

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.2M Amm Acetate, 20%w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.85	α = 90
b = 74.32	β = 94.15
c = 153.32	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	95	CCD	RAYONIX MX300HE		2017-04-15	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	1.78	50.04	98.7	0.072	0.095	0.047	0.998	11.5	4		143943			18.981

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	1.78	1.81	87.9		0.872	0.629	0.445	1.2	2.8

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7DKB	1.86	40.003	127561	6217	99.777	0.173	0.1714	0.2101	27.797

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]
-0.629		0.213	0.059		0.534

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.491
r_dihedral_angle_4_deg	16.081
r_dihedral_angle_3_deg	14.639
r_dihedral_angle_1_deg	6.511
r_lrange_it	5.93
r_lrange_other	5.768
r_scangle_it	4.575
r_scangle_other	4.575
r_mcangle_it	3.106
r_mcangle_other	3.106
r_scbond_it	3.049
r_scbond_other	3.048
r_mcbond_it	2.257
r_mcbond_other	2.255
r_angle_refined_deg	1.613
r_angle_other_deg	1.426
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_refined	0.213
r_nbd_other	0.212
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.164
r_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_xyhbond_nbd_other	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10660
Nucleic Acid Atoms
Solvent Atoms	1361
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data scaling
REFMAC	phasing