3ODV | pdb_00003odv

X-ray structure of kaliotoxin by racemic protein crystallography

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	1.8 M sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.15	α = 109.39
b = 30.511	β = 97.39
c = 41.097	γ = 97.09

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	MARMOSAIC 300 mm CCD		2007-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.95373	APS	23-ID-B

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	0.95	50	88.2	0.057	19.9	4.3	62285	62285

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	0.95	0.98	50.9		1.8	3.5	3600

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	AB INITIO PHASING	THROUGHOUT	0.95	38.13	59134	3130	87.92	0.18878	0.188	0.19	0.20326	0.21	RANDOM	10.564

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]
0.22	0.12	-0.21	-0.53	0.1	0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.988
r_dihedral_angle_4_deg	14.498
r_dihedral_angle_3_deg	13.919
r_dihedral_angle_1_deg	5.446
r_scangle_it	5.161
r_scbond_it	3.483
r_mcangle_it	2.561
r_angle_refined_deg	1.646
r_mcbond_it	1.632
r_rigid_bond_restr	1.232
r_angle_other_deg	0.872
r_mcbond_other	0.449
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	566
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling