8HTW | pdb_00008htw

Crystal Structure of the ring nuclease Sso2081 Y133F mutant from Saccharolobus solfataricus in its apo form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.747	α = 90
b = 95.253	β = 107.803
c = 45.836	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	80	PIXEL	DECTRIS PILATUS3 6M		2022-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.987	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	97.6	0.086	11.6	4.7		24137

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	2.05			1.183

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	THROUGHOUT	7YHL	2	47.626	24114	1177	99.76	0.226	0.2241	0.23	0.2556	0.26	49.345

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]
1.979		1.075	0.663		-2.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.335
r_dihedral_angle_3_deg	13.364
r_lrange_other	11.681
r_lrange_it	11.68
r_scangle_it	9.65
r_scangle_other	9.647
r_mcangle_it	6.889
r_mcangle_other	6.887
r_scbond_it	6.798
r_scbond_other	6.797
r_dihedral_angle_1_deg	6.701
r_mcbond_it	5.225
r_mcbond_other	5.224
r_dihedral_angle_2_deg	4.703
r_angle_refined_deg	1.6
r_angle_other_deg	0.505
r_symmetry_xyhbond_nbd_refined	0.211
r_nbd_other	0.205
r_symmetry_nbd_other	0.185
r_nbd_refined	0.174
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.161
r_symmetry_nbd_refined	0.13
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.072
r_chiral_restr_other	0.037
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2849
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
PHENIX	model building
Coot	model building
HKL-2000	data reduction