2I5S | pdb_00002i5s

Crystal structure of onconase with bound nucleic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION SUPPLEMENTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	41.186596

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.229	α = 90
b = 26.101	β = 90
c = 32.486	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	BRUKER SMART 6000	MONTEL OPTICS	2006-05-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	1.9	64.6145	99.7	0.1249	12.3	9.84		9270

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)
	1.9	1.95	95.9		0.5172	2.52	3.32	624

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		THROUGHOUT	PDB ENTRY 1ONC	1.9	32.49	9229	441	99.719	0.181	0.181	0.178	0.18	0.24	0.25	RANDOM	16.602

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]
-0.207			-0.009		0.216

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.533
r_dihedral_angle_4_deg	20.535
r_dihedral_angle_3_deg	14.183
r_dihedral_angle_1_deg	6.706
r_scangle_it	5.99
r_scbond_it	4.173
r_mcangle_it	2.209
r_angle_refined_deg	1.415
r_mcbond_it	1.361
r_nbtor_refined	0.303
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.15
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_symmetry_hbond_refined	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	826
Nucleic Acid Atoms	41
Solvent Atoms	155
Heterogen Atoms

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction