8SF4

Cystathionine gamma lyase from Thermobifida fusca in internal aldimine form

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5X5H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Well solution comprising 20-30% PEG300, 0.1 M HEPES, 0.2 M MgCl2. 2 uL drops were laid with a 1:1 mixture of well solution and 8 mg/mL protein in 0.1 M HEPES buffer pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.591	α = 90
b = 117.591	β = 90
c = 117.591	γ = 90

Symmetry
Space Group	P 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.978720	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.455	40.003	100	0.075	1	25.36	22.1		94728

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.49	100		1.697	0.748	2.09	21.3

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	1.455	40.003	94728	4687	99.964	0.134	0.133	0.1481	20.789

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.09
r_dihedral_angle_4_deg	20.121
r_dihedral_angle_3_deg	11.996
r_dihedral_angle_1_deg	6.581
r_lrange_it	5.077
r_lrange_other	4.916
r_scangle_other	2.842
r_scangle_it	2.832
r_angle_refined_deg	2.248
r_scbond_it	1.994
r_scbond_other	1.959
r_angle_other_deg	1.679
r_mcangle_other	1.325
r_mcangle_it	1.324
r_mcbond_it	0.96
r_mcbond_other	0.943
r_symmetry_xyhbond_nbd_other	0.282
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_refined	0.227
r_xyhbond_nbd_other	0.223
r_nbtor_refined	0.173
r_nbd_other	0.173
r_symmetry_nbd_other	0.172
r_symmetry_nbd_refined	0.164
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.118
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.038
r_bond_refined_d	0.02
r_gen_planes_refined	0.015
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2835
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	24

Software

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