1Y4L

Crystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	PEG 3350, isopropanol, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.199	α = 90
b = 64.037	β = 90
c = 85.99	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2003-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1

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	30	99.3	0.049				30385	2	2

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	1.7	1.74	97.4		0.507

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	30	30549	28848	1537	99.36	0.227	0.20734	0.20563	0.23955	RANDOM	25.991

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]
-0.97			0.56		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.522
r_dihedral_angle_4_deg	24.038
r_dihedral_angle_3_deg	16.772
r_dihedral_angle_1_deg	5.416
r_scangle_it	2.183
r_mcangle_it	2.087
r_angle_refined_deg	1.663
r_scbond_it	1.384
r_mcbond_it	1.278
r_nbd_refined	0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.522
r_dihedral_angle_4_deg	24.038
r_dihedral_angle_3_deg	16.772
r_dihedral_angle_1_deg	5.416
r_scangle_it	2.183
r_mcangle_it	2.087
r_angle_refined_deg	1.663
r_scbond_it	1.384
r_mcbond_it	1.278
r_nbd_refined	0.332
r_nbtor_refined	0.331
r_xyhbond_nbd_refined	0.233
r_symmetry_hbond_refined	0.232
r_symmetry_vdw_refined	0.181
r_chiral_restr	0.158
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1906
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

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.