7OR6 | pdb_00007or6

The crystal structure of the domain-swapped dimer of onconase

X-RAY DIFFRACTION

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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		298	20% PEG 3350 0.2 M sodium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
	31.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.29	α = 90
b = 60.05	β = 90
c = 101.78	γ = 90

Symmetry
Space Group	P 21 21 21

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	0.9999	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	2.12	51.72	99.9	0.273	1	9.1	12.2		10440

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	2.12	2.15	100		0.7	2.2

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	FREE R-VALUE	1ONC	2.12	51.719	9681	499	92.863	0.188	0.1855	0.19	0.2432	0.24	24.241

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]
0.111			-0.162		0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.901
r_dihedral_angle_4_deg	26.743
r_dihedral_angle_3_deg	18.536
r_dihedral_angle_1_deg	8.978
r_lrange_it	5.955
r_lrange_other	5.905
r_scangle_it	3.967
r_scangle_other	3.966
r_mcangle_other	3.023
r_mcangle_it	3.015
r_scbond_it	2.515
r_scbond_other	2.511
r_mcbond_it	1.82
r_mcbond_other	1.791
r_angle_refined_deg	1.564
r_angle_other_deg	1.278
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.19
r_nbd_other	0.173
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
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	92
Heterogen Atoms

Software

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