7QTA | pdb_00007qta

S1 nuclease from Aspergillus oryzae in complex with uridine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FB9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, protein concentration 10 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.04	α = 107.184
b = 48.186	β = 90.114
c = 65.232	γ = 105.618

Symmetry
Space Group	P 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 PILATUS 6M		2016-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0332	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.06	44.2	86.02	0.085	0.997	8	3.6		187610		-3.7	9.8

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	1.06	1.088	64.47		1.145	0.373	1.2	3.4

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5FB9	1.06	44.2	187610	9423	86.015	0.12	0.1205	0.1181	0.12	0.1468	0.13	Random	13.44

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]
-0.498	-0.01	-0.011	0.272	0.095	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.339
r_dihedral_angle_3_deg	11.128
r_dihedral_angle_4_deg	9.861
r_dihedral_angle_1_deg	6.17
r_dihedral_angle_other_3_deg	4.494
r_rigid_bond_restr	2.495
r_scangle_it	1.914
r_scangle_other	1.914
r_angle_other_deg	1.716
r_scbond_it	1.67
r_angle_refined_deg	1.658
r_mcangle_other	1.308
r_mcangle_it	1.295
r_mcbond_it	1.047
r_mcbond_other	1.031
r_symmetry_nbd_refined	0.243
r_nbd_refined	0.233
r_nbd_other	0.207
r_nbtor_refined	0.183
r_symmetry_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.142
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.104
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.011
r_bond_other_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4075
Nucleic Acid Atoms
Solvent Atoms	770
Heterogen Atoms	135

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building