1W8O

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 = 46.712α = 90
b = 111.168β = 90
c = 142.195γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2003-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.743.6920.0714.84824206
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)
11.71.79720.324.43.8

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 1EUT1.787.7174228390994.80.1640.1620.197RANDOM19.07
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]
0.45-0.14-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg12.229
r_dihedral_angle_1_deg6.553
r_scangle_it4.632
r_scbond_it2.948
r_mcangle_it2.041
r_angle_refined_deg1.848
r_mcbond_it1.244
r_angle_other_deg1.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg12.229
r_dihedral_angle_1_deg6.553
r_scangle_it4.632
r_scbond_it2.948
r_mcangle_it2.041
r_angle_refined_deg1.848
r_mcbond_it1.244
r_angle_other_deg1.014
r_symmetry_vdw_refined0.29
r_symmetry_vdw_other0.283
r_nbd_other0.202
r_nbd_refined0.197
r_symmetry_hbond_refined0.193
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.169
r_chiral_restr0.141
r_nbtor_other0.086
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms709
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing