1KV0 | pdb_00001kv0

Cis/trans Isomerization of Non-prolyl Peptide Bond Observed in Crystal Structure of an Scorpion Toxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SN1	PDB entry 1SN1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	ammonium sulfate, Tris-HCl, Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.758	α = 90
b = 32.758	β = 90
c = 176.822	γ = 120

Symmetry
Space Group	P 31 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	293	CCD	ADSC QUANTUM 4		2000-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-18B	1.0	Photon Factory	BL-18B

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	1.4	29.3	85.8	0.04				19260

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)
	1.4	1.48	74.6		0.201	3.6

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	PDB entry 1SN1	1.4	29.49	19260	17355	1898	100	0.14416	0.14194	0.15	0.16448	0.17	RANDOM	15.774

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]
0.29	0.14		0.29		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	9.308
r_dihedral_angle_1_deg	5.699
r_scangle_it	5.59
r_scbond_it	3.705
r_sphericity_bonded	3.416
r_mcangle_it	3.069
r_angle_refined_deg	1.986
r_rigid_bond_restr	1.901
r_mcbond_it	1.873
r_angle_other_deg	1.086
r_symmetry_vdw_other	0.35
r_nbd_other	0.283
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.153
r_xyhbond_nbd_refined	0.141
r_nbtor_other	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_xyhbond_nbd_other
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1041
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling