1W8N

Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora viridifaciens.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EUTPDB ENTRY 1EUT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
116 % PEG 3350, 0.2M AMMONIUM CITRATE.
Crystal Properties
Matthews coefficientSolvent content
2.854.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.602α = 90
b = 111.608β = 90
c = 143.865γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU-MSCOSMIC MIRRORS2003-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.119.92890.076.95.6446976

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 1EUT2.187.7137473198488.10.1680.1660.219RANDOM23.41
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]
-0.58-0.080.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.218
r_scangle_it3.541
r_scbond_it2.356
r_angle_refined_deg1.773
r_mcangle_it1.483
r_mcbond_it0.929
r_angle_other_deg0.909
r_symmetry_vdw_other0.312
r_symmetry_vdw_refined0.293
r_nbd_other0.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.218
r_scangle_it3.541
r_scbond_it2.356
r_angle_refined_deg1.773
r_mcangle_it1.483
r_mcbond_it0.929
r_angle_other_deg0.909
r_symmetry_vdw_other0.312
r_symmetry_vdw_refined0.293
r_nbd_other0.266
r_symmetry_hbond_refined0.225
r_nbd_refined0.206
r_xyhbond_nbd_refined0.2
r_chiral_restr0.104
r_nbtor_other0.091
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms4531
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing