3PLC | pdb_00003plc

Crystal structure of Beta-Cardiotoxin, a novel three-finger cardiotoxin from the venom of Ophiophagus hannah

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapour diffusion, hanging drop	7	298	25% (w/v) PEG 1500, Spermidine additive, pH 7, vapour diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.949	α = 90
b = 58.949	β = 90
c = 53.026	γ = 120

Symmetry
Space Group	P 31

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	Bruker AXIOM 200		2009-11-18		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.41	50.01	99.6	0.137	5.6	11.1		7999

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	2.41	2.5	96		0.484		8.9	784

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1KXI	2.41	50	7983	787	99.63	0.2373	0.234	0.24	0.2666	0.28	RANDOM	45.967

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]
-9.93			-9.93		19.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.775
r_dihedral_angle_3_deg	22.531
r_dihedral_angle_4_deg	20.035
r_dihedral_angle_1_deg	8.675
r_scangle_it	3.712
r_scbond_it	2.146
r_mcangle_it	2.123
r_angle_refined_deg	1.896
r_mcbond_it	1.169
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.775
r_dihedral_angle_3_deg	22.531
r_dihedral_angle_4_deg	20.035
r_dihedral_angle_1_deg	8.675
r_scangle_it	3.712
r_scbond_it	2.146
r_mcangle_it	2.123
r_angle_refined_deg	1.896
r_mcbond_it	1.169
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1293
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.