8QNO | pdb_00008qno

Crystal structure of S-adenosyl-L-homocysteine hydrolase treated at 368 K from Pyrococcus furiosus in complex with inosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7R37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	Before crystallization, enzyme was heat treated at 95 degree celsius (or 368 Kelvin). 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.714	α = 90
b = 111.714	β = 90
c = 122.11	γ = 90

Symmetry
Space Group	P 42 21 2

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		2023-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.28022	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.033	48.31	99.71	0.2373	0.0466	0.99	15.36	26.8		50113			33.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.033	2.106			0.681

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.033	48.308	50111	2507	99.749	0.157	0.1547	0.17	0.2032	0.21	34.257

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]
0.03			0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.95
r_dihedral_angle_6_deg	15.093
r_dihedral_angle_2_deg	10.418
r_lrange_it	7.67
r_lrange_other	7.668
r_dihedral_angle_1_deg	6.452
r_scangle_it	6.423
r_scangle_other	6.423
r_scbond_it	4.218
r_scbond_other	4.218
r_mcangle_it	3.392
r_mcangle_other	3.392
r_mcbond_it	2.452
r_mcbond_other	2.45
r_angle_refined_deg	1.425
r_angle_other_deg	0.467
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.176
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.074
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_dihedral_angle_other_2_deg	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	6648
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AutoSol	phasing