7YLZ | pdb_00007ylz

Unliganded form of hydroxyamidotransferase TsnB9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	30% (w/v) PEG 8,000, 0.2 M ammonium sulfate, and 0.1 M sodium cacodylate trihydrate (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.68	α = 101.153
b = 76.57	β = 114.435
c = 82.14	γ = 109.556

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 PILATUS 2M-F		2020-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.72	50	91.8	0.099	0.986	6.42	1.9		64632

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.72	2.79			0.615	0.702	1.14

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	FREE R-VALUE	AlphaFold model	2.72	33.611	33710	1691	96.207	0.268	0.2661	0.27	0.2937	0.3	35.863

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]
0.407	0.538	-1.021	3.152	0.37	-1.944

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.749
r_dihedral_angle_3_deg	13.758
r_dihedral_angle_4_deg	13.594
r_dihedral_angle_1_deg	5.091
r_lrange_it	1.363
r_lrange_other	1.363
r_angle_refined_deg	1.187
r_angle_other_deg	1.086
r_mcangle_it	0.389
r_mcangle_other	0.389
r_mcbond_it	0.204
r_mcbond_other	0.204
r_scangle_it	0.166
r_scangle_other	0.165
r_nbd_refined	0.16
r_symmetry_nbd_other	0.157
r_nbtor_refined	0.146
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbd_refined	0.097
r_symmetry_nbtor_other	0.073
r_scbond_it	0.066
r_scbond_other	0.063
r_chiral_restr	0.032
r_symmetry_xyhbond_nbd_other	0.004
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8691
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	50

Software

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