8VDY

Crystal Structure of Delta 114-117 D-Dopachrome Tautomerase (D-DT)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	26-32% PEG 3350, 0.25-0.275M Ammonium Acetate.

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.533	α = 90
b = 59.529	β = 107.93
c = 129.976	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	290	PIXEL	DECTRIS PILATUS3 S 6M		2023-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11583	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.44	89.84	99.8	0.267	0.953	4.5	3.4		51582

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.44	2.48	99.7		1.363	0.25	1	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.44	89.84	51582	2702	99.65	0.25138	0.24878	0.30177	RANDOM	27.14

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]
-0.01		-0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.268
r_dihedral_angle_4_deg	18.015
r_dihedral_angle_3_deg	17.944
r_dihedral_angle_1_deg	6.025
r_long_range_B_refined	4.861
r_long_range_B_other	4.86
r_mcangle_it	3.237
r_mcangle_other	3.237
r_scangle_other	2.965
r_angle_other_deg	2.541
r_mcbond_it	2.041
r_mcbond_other	2.041
r_scbond_it	1.836
r_scbond_other	1.836
r_angle_refined_deg	1.567
r_chiral_restr	0.066
r_bond_other_d	0.036
r_bond_refined_d	0.008
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9380
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

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