3HG6 | pdb_00003hg6

Crystal Structure of the Recombinant Onconase from Rana pipiens

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	capillary contradiffusion	4	288	4 M Ammonium sulphate and 0.1 M sodium acetate, capillary contradiffusion, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.516	α = 90
b = 39.799	β = 90
c = 68.536	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	CCD	MAR CCD 165 mm		2008-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.90750	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	14.7	95.5	0.128	0.128	15.403	12.8		9807			18.879

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	83.6		0.498	0.498	3.84	10.8	838

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1ONC	1.7	14.7	10286	9772	472	95.41	0.187	0.185	0.202	0.237	0.2432	RANDOM	14.796

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]
-2.8			4.99		-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.03
r_dihedral_angle_4_deg	24.598
r_dihedral_angle_3_deg	14.383
r_dihedral_angle_1_deg	7.348
r_scangle_it	5.218
r_scbond_it	3.698
r_mcangle_it	2.253
r_angle_refined_deg	2.221
r_mcbond_it	1.579
r_chiral_restr	0.144
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	826
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	26

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling