1N1Y

Trypanosoma rangeli sialidase in complex with sialic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N1S	pdb entry 1n1s

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	PEG-8000, sodium cacodylate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.833	α = 90
b = 95.639	β = 90
c = 109.218	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	ADSC QUANTUM 4		2000-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	2.8	50	92.6	0.098		5		18969

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)
	2.8	2.9	83.5		0.267

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 entry 1n1s	2.8	15	17813	17813	962	92.72	0.2369	0.23692	0.23518	0.26917	RANDOM	34.828

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]
-0.09			-2.24		2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.762
r_dihedral_angle_1_deg	2.595
r_angle_refined_deg	1.969
r_nbd_refined	0.238
r_mcangle_it	0.142
r_symmetry_vdw_refined	0.136
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.095
r_mcbond_it	0.079
r_scangle_it	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.762
r_dihedral_angle_1_deg	2.595
r_angle_refined_deg	1.969
r_nbd_refined	0.238
r_mcangle_it	0.142
r_symmetry_vdw_refined	0.136
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.095
r_mcbond_it	0.079
r_scangle_it	0.072
r_chiral_restr	0.066
r_scbond_it	0.039
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4816
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	21

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.