7DKD

Stenotrophomonas maltophilia DPP7 in complex with Asn-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 Ca Acetate, 20%w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.552	α = 90
b = 74.892	β = 94.502
c = 154.647	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	PIXEL	DECTRIS EIGER X 16M		2019-01-27	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)	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	1.92	50.48	99.7	0.186	0.076	0.989	7.4	6.9		119220			14.452

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	1.92	1.95	94.8		1.199	0.485	0.632	2	7

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	1.92	40.003	119144	6098	99.805	0.205	0.2022	0.2478	30.137

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]
-0.664		0.211	-0.265		0.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.709
r_dihedral_angle_3_deg	15.699
r_dihedral_angle_4_deg	14.819
r_dihedral_angle_1_deg	6.661
r_lrange_it	6.392
r_lrange_other	6.206
r_scangle_it	4.078
r_scangle_other	4.078
r_mcangle_it	3.695
r_mcangle_other	3.695
r_scbond_it	2.581
r_scbond_other	2.581
r_mcbond_it	2.477
r_mcbond_other	2.476
r_angle_refined_deg	1.554
r_angle_other_deg	1.318
r_nbd_refined	0.208
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.164
r_nbd_other	0.154
r_symmetry_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.15
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_bond_refined_d	0.009
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	10660
Nucleic Acid Atoms
Solvent Atoms	1162
Heterogen Atoms	60

Software

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