1MZ6

Trypanosoma rangeli sialidase in complex with the inhibitor DANA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MZ5	Unliganded T. rangeli sialidase 1MZ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG-8000, ammonium sulfate, morpholinoethanesulfonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.2	α = 90
b = 93.8	β = 90
c = 105.3	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	IMAGE PLATE	MARRESEARCH		1997-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LURE BEAMLINE D41A	1.375	LURE	D41A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.9	15	99.9	0.138		6.6	17063	17063

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	99.8		0.306

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	Unliganded T. rangeli sialidase 1MZ5	2.9	15	16159	16159	869	99.26	0.20884	0.20884	0.20466	0.28689	RANDOM	22.262

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]
0.46			-0.32		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	23.086
r_dihedral_angle_1_deg	4.585
r_scangle_it	3.041
r_angle_refined_deg	2.395
r_scbond_it	1.818
r_mcangle_it	1.121
r_mcbond_it	0.594
r_symmetry_vdw_refined	0.288
r_nbd_refined	0.283
r_xyhbond_nbd_refined	0.173

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	23.086
r_dihedral_angle_1_deg	4.585
r_scangle_it	3.041
r_angle_refined_deg	2.395
r_scbond_it	1.818
r_mcangle_it	1.121
r_mcbond_it	0.594
r_symmetry_vdw_refined	0.288
r_nbd_refined	0.283
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.143
r_symmetry_hbond_refined	0.075
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4759
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	90

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.