6TRG | pdb_00006trg

Salmonella typhimurium neuraminidase mutant (D100S)

X-RAY DIFFRACTION

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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 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.17	α = 90
b = 81.636	β = 90
c = 91.148	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		2001-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.80	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	30.885	98.3	0.999	15	5		186230			6.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.02	96		0.905	2	3.5

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	1	30.885	186230	9182	98.062	0.101	0.1007	0.1	0.1161	0.12	9.881

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]
0.338			-0.285		-0.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.784
r_dihedral_angle_4_deg	18.27
r_dihedral_angle_3_deg	13.122
r_dihedral_angle_1_deg	8.004
r_rigid_bond_restr	5.215
r_lrange_it	3.01
r_lrange_other	2.59
r_scangle_it	2.561
r_scangle_other	2.554
r_scbond_other	2.535
r_scbond_it	2.532
r_angle_refined_deg	2.381
r_angle_other_deg	1.618
r_mcangle_it	1.589
r_mcangle_other	1.589
r_mcbond_it	1.181
r_mcbond_other	1.18
r_symmetry_nbd_refined	0.394
r_nbd_other	0.372
r_nbd_refined	0.305
r_symmetry_xyhbond_nbd_refined	0.304
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.132
r_symmetry_nbtor_other	0.086
r_xyhbond_nbd_other	0.067
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2937
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	60

Software

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