2C4L

Structure of Neuraminidase Subtype N9 Complexed with 30 MM Sialic Acid (NANA, NEU5AC), Crystal Soaked for 24 Hours at 291 K and Finally Backsoaked for 30 Min in a Cryoprotectant Solution which did not contain NEU5AC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NN9PDB ENTRY 7NN9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8PROTEIN WAS CRYSTALLISED FROM 1.9M POTASSIUM PHOSPHATE PH 6.8, THEN SOAKED FOR 24 HOURS IN 30 MM NEU5AC AND FINALLY BACKSOAKED FOR 30 MIN IN A CRYOPROTECTANT SOLUTION WHICH DID NOT CONTAIN NEU5AC
Crystal Properties
Matthews coefficientSolvent content
2.9458.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.178α = 90
b = 181.178β = 90
c = 181.178γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateCONFOCAL OSMIC BLUE2004-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1542.71000.116.110.72782019.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.211000.342.210.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 7NN92.1542.72637013961000.1570.1550.196RANDOM15.06
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg19.563
r_dihedral_angle_3_deg13.006
r_dihedral_angle_1_deg7.603
r_scangle_it2.934
r_scbond_it1.984
r_angle_refined_deg1.612
r_mcangle_it1.092
r_mcbond_it0.684
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg19.563
r_dihedral_angle_3_deg13.006
r_dihedral_angle_1_deg7.603
r_scangle_it2.934
r_scbond_it1.984
r_angle_refined_deg1.612
r_mcangle_it1.092
r_mcbond_it0.684
r_nbtor_refined0.309
r_nbd_refined0.285
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.14
r_chiral_restr0.111
r_symmetry_hbond_refined0.104
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3067
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing