7QTB

S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate

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
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.075	α = 107.47
b = 48.459	β = 90.076
c = 65.547	γ = 105.702

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	1.04	44.358	84.5	0.053	0.999	10.8	3.6		196791		-3.7	6.6

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	1.04	1.06	42.2		0.505	0.829

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5FB9	1.04	44.358	196789	9747	84.456	0.11	0.1097	0.1087	0.1307	Random	11.107

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]
0.041	-0.043	0.01	0.024	-0.048	-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.446
r_dihedral_angle_3_deg	10.802
r_dihedral_angle_4_deg	8.625
r_dihedral_angle_1_deg	6.279
r_rigid_bond_restr	2.574
r_angle_refined_deg	1.775
r_angle_other_deg	1.717
r_scangle_it	1.687
r_scangle_other	1.687
r_scbond_it	1.514
r_mcangle_other	1.039
r_mcangle_it	1.03
r_mcbond_other	0.843
r_mcbond_it	0.832
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.229
r_nbd_other	0.202
r_nbtor_refined	0.186
r_symmetry_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.131
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr_other	0.035
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4075
Nucleic Acid Atoms
Solvent Atoms	898
Heterogen Atoms	175

Software

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