8OVH

Crystal structure of O-acetyl-L-homoserine sulfhydrolase from Saccharomyces cerevisiae in complex with Pyridoxal-5'-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	22% (w/v) PEG 6000, 200 mM LiCl, and 100 mM sodium acetate, pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.579	α = 90
b = 118.218	β = 92.908
c = 131.381	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	100	PIXEL	DECTRIS EIGER X 16M		2022-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.17	49.59	97.46	0.18	0.99	7.7	6.5		629183

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	2.17	2.21			1.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.171	49.59	96652	4833	97.447	0.175	0.1715	0.2376	52.594

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]
-0.078		0.034	-0.051		0.125

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.866
r_dihedral_angle_3_deg	15.562
r_lrange_other	11.263
r_lrange_it	11.257
r_scangle_it	8.852
r_scangle_other	8.852
r_dihedral_angle_2_deg	7.834
r_dihedral_angle_1_deg	7.643
r_mcangle_other	7.343
r_mcangle_it	7.342
r_scbond_it	6.072
r_scbond_other	6.071
r_mcbond_it	5.224
r_mcbond_other	5.22
r_angle_refined_deg	1.592
r_angle_other_deg	0.516
r_symmetry_nbd_refined	0.329
r_nbd_other	0.221
r_nbd_refined	0.22
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_refined	0.07
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12380
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing