7AEY | pdb_00007aey

Salmonella typhimurium neuraminidase in complex with isocarba-DANA.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes. A 2.5mM solution of isocarba-DANA was then soaked into the resultant crystals for 90 minutes at a temperature of 293K.

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.089	α = 90
b = 81.375	β = 90
c = 90.857	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	MAR scanner 345 mm plate		1998-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.79	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	0.918	24.325	97.8	0.07	0.078	19.78	3.5		236859

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.92	0.94	82		0.393	0.511	1.97	1.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3SIL	0.919	24.321	236762	11838	97.675	0.1	0.0988	0.0987	0.1151	0.115	8.866

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]
-0.045			-0.243		0.288

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.391
r_dihedral_angle_4_deg	15.387
r_dihedral_angle_3_deg	13.306
r_dihedral_angle_1_deg	8.386
r_mcangle_it	7.063
r_mcangle_other	7.062
r_lrange_it	6.63
r_lrange_other	6.173
r_rigid_bond_restr	5.706
r_mcbond_other	5.139
r_mcbond_it	5.138
r_scangle_it	3.226
r_scangle_other	3.209
r_scbond_it	2.569
r_scbond_other	2.562
r_angle_refined_deg	2.346
r_angle_other_deg	1.659
r_symmetry_xyhbond_nbd_refined	0.371
r_nbd_refined	0.313
r_symmetry_nbd_refined	0.294
r_xyhbond_nbd_refined	0.258
r_nbd_other	0.239
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.174
r_xyhbond_nbd_other	0.146
r_chiral_restr	0.14
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2940
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing