2V4C

Structure of sialic acid binding protein (SiaP) in the presence of KDN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B50PDB ENTRY 3B50

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727736 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, 10 MM KDN, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0 28.5% PEG 6K); TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.399α = 90
b = 74.502β = 90
c = 86.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.75099.20.0917.56.534122
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)
11.71.7393.90.442.435.2

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 3B501.741.5632329171198.750.14570.143090.19397RANDOM21.302
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]
-0.070.09-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.142
r_dihedral_angle_3_deg14.998
r_dihedral_angle_4_deg9.095
r_dihedral_angle_1_deg5.427
r_scangle_it5.153
r_scbond_it4.268
r_mcangle_it2.153
r_angle_refined_deg1.567
r_mcbond_it1.359
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.142
r_dihedral_angle_3_deg14.998
r_dihedral_angle_4_deg9.095
r_dihedral_angle_1_deg5.427
r_scangle_it5.153
r_scbond_it4.268
r_mcangle_it2.153
r_angle_refined_deg1.567
r_mcbond_it1.359
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2439
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing