7ORD

The crystal structure of the domain-swapped dimer of onconase (2)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ONC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1 M Tris-HCl pH 8.5 25% PEG 3350 0.2 M Ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.75	α = 90
b = 28.54	β = 94.24
c = 61.48	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	100	PIXEL	DECTRIS PILATUS 6M		2020-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1	ELETTRA	11.2C

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	2.14	58.59	97.4	0.124	1	10.6	5.9		11313

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	2.14	2.18			0.6	2.3	4.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1ONC	2.14	58.59	10936	526	94.081	0.214	0.2118	0.2668	29.169

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]
-0.428		0.077	-0.043		0.455

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.359
r_dihedral_angle_4_deg	22.241
r_dihedral_angle_3_deg	17.051
r_lrange_it	8.414
r_dihedral_angle_1_deg	8.353
r_lrange_other	8.305
r_scangle_it	5.132
r_scangle_other	5.128
r_mcangle_it	3.996
r_mcangle_other	3.994
r_scbond_it	3.248
r_scbond_other	3.231
r_mcbond_other	2.475
r_mcbond_it	2.474
r_angle_refined_deg	1.636
r_angle_other_deg	1.235
r_nbd_other	0.248
r_symmetry_nbd_refined	0.244
r_xyhbond_nbd_refined	0.224
r_nbd_refined	0.204
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.051
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1652
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing