2H5F | pdb_00002h5f

Denmotoxin: A the three-finger toxin from colubrid snake Boiga dendrophila with bird-specific activity

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	291	1.2M Na, KPO4, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.91	α = 90
b = 34.038	β = 118.36
c = 54.377	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	ADSC QUANTUM 210		2004-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.006768	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	52	93.5				50240

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.74	72.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	47.67	12080	11487	584	94.19	0.20373	0.20188	0.2089	0.2384	0.2324	RANDOM	15.878

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]
1.31		0.43	-0.4		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.098
r_dihedral_angle_1_deg	5.561
r_scbond_it	4.235
r_mcangle_it	3.727
r_angle_refined_deg	2.088
r_mcbond_it	2.079
r_angle_other_deg	1.036
r_nbd_refined	0.363
r_symmetry_vdw_other	0.329
r_nbd_other	0.311
r_symmetry_vdw_refined	0.299
r_symmetry_hbond_refined	0.263
r_xyhbond_nbd_refined	0.231
r_chiral_restr	0.148
r_nbtor_other	0.095
r_metal_ion_refined	0.071
r_bond_refined_d	0.032
r_bond_other_d	0.021
r_gen_planes_refined	0.011
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1135
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
MOLREP	phasing