2F9R

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XX1	PDB code: 1XX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	11	298	2.4 M trisodium citrate, pH 11, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.587	α = 90
b = 140.587	β = 90
c = 113.608	γ = 120

Symmetry
Space Group	P 65

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		2005-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.478	LNLS	D03B-MX1

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	1.85	22.5	83.47			90483	86016		2

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	1.85	1.89	83.3

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code: 1XX1	1.85	20	90483	86016	4467	83.47	0.225	0.18959	0.18729	0.23398	RANDOM	24.157

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]
0.66	0.33		0.66		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.645
r_dihedral_angle_4_deg	16.231
r_dihedral_angle_3_deg	14.406
r_dihedral_angle_1_deg	6.23
r_scangle_it	3.735
r_scbond_it	2.674
r_mcangle_it	1.661
r_angle_refined_deg	1.34
r_mcbond_it	1.038
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.645
r_dihedral_angle_4_deg	16.231
r_dihedral_angle_3_deg	14.406
r_dihedral_angle_1_deg	6.23
r_scangle_it	3.735
r_scbond_it	2.674
r_mcangle_it	1.661
r_angle_refined_deg	1.34
r_mcbond_it	1.038
r_nbtor_refined	0.319
r_nbd_refined	0.217
r_metal_ion_refined	0.217
r_symmetry_hbond_refined	0.19
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9076
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
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.