2Q0R | pdb_00002q0r

Structure of Pectenotoxin-2 Bound to Actin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ASO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	100 mM Na/MES/acetate, pH 5.5, 15% methyl ether poly(ethylene glycol) 5000, 10% hexanediol, 30 mM CaCl2, and 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.437	α = 90
b = 56.856	β = 90.16
c = 105.747	γ = 90

Symmetry
Space Group	C 1 2 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	SBC	Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2006-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.96411	APS	19-BM

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	1.7	45	97.2	0.04	14.4	4.2		37755			23.4

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)
	1.7	1.76	93.4		0.109	9.5	3.9	3595

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	2ASO	1.7	45	157276	37752	1887	96.98	0.17	0.168	0.18	0.204	0.21	RANDOM	14.099

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]
0.65		-0.02	-0.92		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.838
r_dihedral_angle_4_deg	17.102
r_dihedral_angle_3_deg	12.715
r_dihedral_angle_1_deg	5.498
r_scangle_it	3.011
r_scbond_it	2.069
r_angle_refined_deg	1.772
r_angle_other_deg	1.321
r_mcangle_it	1.269
r_mcbond_it	0.822
r_symmetry_vdw_refined	0.393
r_nbd_refined	0.22
r_symmetry_vdw_other	0.22
r_mcbond_other	0.2
r_nbd_other	0.187
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.159
r_nbtor_other	0.089
r_chiral_restr	0.087
r_metal_ion_refined	0.079
r_symmetry_metal_ion_refined	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2780
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	96

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction