9IFB | pdb_00009ifb

Crystal structure of S-adenosyl-L-homocysteine hydrolase mutant C221W 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	comprising 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.066	α = 90
b = 112.066	β = 90
c = 121.97	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		2020-12-05	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	2.53	112.07	99.9	0.19	0.99	10.5	13.5		26591

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	2.53	2.63			0.81

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	2.53	82.522	26547	1352	99.88	0.158	0.1548	0.1618	0.2167	0.2202	40.674

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]
0.756			0.756		-1.512

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.06
r_dihedral_angle_6_deg	14.789
r_lrange_it	8.267
r_lrange_other	8.267
r_dihedral_angle_2_deg	7.885
r_scangle_it	6.996
r_scangle_other	6.995
r_dihedral_angle_1_deg	6.78
r_scbond_it	4.625
r_scbond_other	4.624
r_mcangle_it	4.609
r_mcangle_other	4.609
r_mcbond_it	3.189
r_mcbond_other	3.188
r_angle_refined_deg	1.74
r_angle_other_deg	0.579
r_nbd_refined	0.211
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.18
r_nbd_other	0.17
r_symmetry_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_ncsr_local_group_1	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6664
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	76

Software

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