9O3U | pdb_00009o3u

Crystal Structure of K109A Variant of D-Dopachrome Tautomerase (D-DT)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DPT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M Sodium malonate pH 4.0, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.723	α = 90
b = 94.45	β = 105.345
c = 95.253	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	90	PIXEL	DECTRIS PILATUS3 6M		2024-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11584	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.43	94.45	99.95	0.998	9.9	6.6		229968

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.53	99.99		0.099

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.49	72.163	197304	10237	99.951	0.186	0.1848	0.1846	0.2165	0.2163	18.395

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]
0.001			-0.003		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.891
r_dihedral_angle_4_deg	17.689
r_dihedral_angle_3_deg	12.216
r_dihedral_angle_1_deg	6.759
r_lrange_it	4.427
r_lrange_other	4.187
r_scangle_it	3.097
r_scangle_other	3.097
r_angle_other_deg	2.481
r_scbond_it	2.129
r_scbond_other	2.129
r_mcangle_it	2.046
r_mcangle_other	2.046
r_angle_refined_deg	1.635
r_mcbond_it	1.501
r_mcbond_other	1.501
r_nbd_other	0.242
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.218
r_nbd_refined	0.21
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.131
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.071
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.015
r_gen_planes_other	0.013
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10438
Nucleic Acid Atoms
Solvent Atoms	1487
Heterogen Atoms	77

Software

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