2OSH | pdb_00002osh

crystal structure of Natratoxin, a snake sPLA2 that blocks A-type K+ channel

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MF4	PDB ENTRY 1MF4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	281	2.0M Ammonium Sulfate, 5% v/v iso-Propano, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.078	α = 90
b = 42.078	β = 90
c = 64.117	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.2	20	97.4	0.052	0.052	2.8	2	5731	5557	1	1	19.3

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)
	2.2	2.32	98.7		0.127	0.127	3.5	2	809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 1MF4	2.2	20	1	5731	5557	266	96.96	0.192	0.19	0.1894	0.242	0.2346	RANDOM	19.297

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]
0.51			0.51		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.077
r_dihedral_angle_4_deg	18.517
r_dihedral_angle_3_deg	16.416
r_dihedral_angle_1_deg	5.652
r_scangle_it	2.436
r_scbond_it	1.686
r_angle_refined_deg	1.244
r_mcangle_it	1.205
r_mcbond_it	0.706
r_symmetry_hbond_refined	0.333
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	908
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling