7SVL | pdb_00007svl

DPP9 IN COMPLEX WITH LIGAND ICeD-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EOQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	10% PEG 8000 25% Glycerol 0.16 M Calcium Acetate 0.08 M Cacodilate pH 6.25

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.716	α = 90
b = 117.398	β = 105.6
c = 163.691	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	PIXEL	DECTRIS PILATUS 6M		2019-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.9998	SRS	PX10.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.46	157.66	95.6	0.103	6.1	1.9		151376

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.46	2.524	97.28		0.597		2

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 (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	6EOQ	2.46	157.66	150372	1004	95.61	0.2635	0.263	0.2661	0.3409	0.3404	RANDOM	39.204

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]
-2.46		-0.43	2.51		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.811
r_dihedral_angle_4_deg	18.422
r_dihedral_angle_3_deg	15.262
r_dihedral_angle_1_deg	5.425
r_angle_other_deg	2.59
r_angle_refined_deg	1.568
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26814
Nucleic Acid Atoms
Solvent Atoms	1031
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing