7DKB

Stenotrophomonas maltophilia DPP7 in complex with Val-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
2.43	49.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.49	α = 90
b = 73.33	β = 95.16
c = 151.82	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		2015-10-02	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	1.94	45.75	93.7	0.256	0.275	0.1	0.397	7.9	7.6		100498			18.556

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	1.94	1.97	60.1		1.487	0.576	0.397	1.4	7.5

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	3WOL	2.03	40	91951	4522	97.619	0.203	0.2009	0.2454	29.45

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]
0.867		0.443	0.819		-1.738

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.28
r_dihedral_angle_4_deg	17.156
r_dihedral_angle_3_deg	16.906
r_dihedral_angle_1_deg	6.904
r_lrange_it	5.801
r_lrange_other	5.783
r_scangle_it	4.485
r_scangle_other	4.485
r_mcangle_it	3.215
r_mcangle_other	3.215
r_scbond_it	2.891
r_scbond_other	2.891
r_mcbond_it	2.214
r_mcbond_other	2.214
r_angle_refined_deg	1.576
r_angle_other_deg	1.366
r_symmetry_xyhbond_nbd_refined	0.27
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.211
r_nbd_other	0.196
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_other	0.1
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10658
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	40

Software

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