6XIX | pdb_00006xix

Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	1 uL 20 mg/mL protein + 1 uL 24% PEG6000, 0.1 M Bis-Tris propane

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.95	α = 118.403
b = 76.55	β = 89.606
c = 93.59	γ = 103.065

Symmetry
Space Group	P 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 EIGER X 16M		2018-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979	APS	24-ID-E

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	2.1	81.57	90.4	0.068	9.16	2.13		91216

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	2.1	2.2	92.2		0.176	4.76	2.16

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 6AZO	2.1	70.57	91215	4561	90.669	0.181	0.1785	0.19	0.2283	0.24	20.286

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]
1.444	0.129	-2.53	-0.294	-0.795	0.251

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.83
r_dihedral_angle_other_3_deg	28.14
r_dihedral_angle_4_deg	18.848
r_dihedral_angle_3_deg	14.997
r_dihedral_angle_1_deg	7.014
r_lrange_it	4.519
r_lrange_other	4.428
r_scangle_it	3.191
r_scangle_other	3.19
r_mcangle_it	2.25
r_mcangle_other	2.25
r_scbond_it	2.033
r_scbond_other	2.033
r_angle_refined_deg	1.561
r_mcbond_it	1.478
r_mcbond_other	1.478
r_angle_other_deg	1.292
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.196
r_nbd_other	0.196
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.152
r_symmetry_nbd_refined	0.143
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13411
Nucleic Acid Atoms
Solvent Atoms	783
Heterogen Atoms	32

Software

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