2P6Z | pdb_00002p6z

Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Amphinase-2 (native)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	289	protein: 12.5 mg/ml, PEG 4000 30%, Na Citrate 0.1 M, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.795	α = 116.56
b = 44.607	β = 83.19
c = 46.054	γ = 103.68

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	CCD	MAR CCD 165 mm	mirrors	2006-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	1.91	41.2	89.8	0.037	18.8	2.1	15432	14385	2	1	15

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)
	1.91	2.01	63.5		0.108	7.5	1.9	1477

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	Amphinase-2 (native)	1.93	41.2	15432	14385	727	93.24	0.148	0.148	0.146	0.145	0.191	0.1895	RANDOM	14.63

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]
0.18	-1.18	-1.02	-0.18	0.05	-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.762
r_dihedral_angle_4_deg	14.339
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	7.046
r_scangle_it	2.776
r_scbond_it	1.708
r_angle_refined_deg	1.224
r_mcangle_it	0.932
r_mcbond_it	0.485
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.762
r_dihedral_angle_4_deg	14.339
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	7.046
r_scangle_it	2.776
r_scbond_it	1.708
r_angle_refined_deg	1.224
r_mcangle_it	0.932
r_mcbond_it	0.485
r_nbtor_refined	0.292
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.186
r_symmetry_vdw_refined	0.158
r_metal_ion_refined	0.148
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1797
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	42

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.