6XJE | pdb_00006xje

Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with triuret

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	1 uL 20 mg/mL protein + 1 uL 24% w/v PEG6000, 0.1 M Bis-Tris propane, 1 mM triuret, pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.53	α = 90
b = 114.44	β = 90
c = 142.93	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033320	APS	23-ID-D

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	1.45	60.62	100	0.051	20.99	7.47		150183

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	1.45	1.55	100		0.547	3.97	7.21

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 6XIX	1.45	60.616	150183	7510	99.957	0.173	0.172	0.17	0.1898	0.19	19.158

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]
-0.08			-0.549		0.629

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.706
r_dihedral_angle_4_deg	17.324
r_dihedral_angle_3_deg	12.733
r_dihedral_angle_1_deg	6.367
r_lrange_it	5.318
r_lrange_other	5.318
r_scangle_it	4.546
r_scangle_other	4.546
r_scbond_it	3.083
r_scbond_other	3.083
r_mcangle_other	2.359
r_mcangle_it	2.356
r_angle_refined_deg	1.873
r_mcbond_it	1.703
r_mcbond_other	1.696
r_angle_other_deg	1.594
r_nbd_other	0.225
r_nbd_refined	0.219
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.142
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.101
r_ncsr_local_group_3	0.1
r_ncsr_local_group_6	0.093
r_ncsr_local_group_4	0.087
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_5	0.084
r_ncsr_local_group_1	0.081
r_ncsr_local_group_2	0.079
r_gen_planes_refined	0.02
r_bond_refined_d	0.013
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6698
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building