2WX9

Crystal structure of the sialic acid binding periplasmic protein SiaP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V4CPDB ENTRY 2V4C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727736 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL,AND NEU5GC PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0, 28.5% PEG 6K, 3% W/V 1,5-DIAMINOPENTANE DIHYDROCHLORIDE) TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.73α = 90
b = 74.49β = 90
c = 87.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.3732.251000.0812.87623792
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)
11.371.451000.622.56.8

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 2V4C1.3732.256237933361000.1180.1160.1582V4C9.88
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]
-0.2-0.220.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.939
r_dihedral_angle_3_deg12.18
r_dihedral_angle_4_deg9.021
r_dihedral_angle_1_deg5.67
r_scangle_it5.108
r_scbond_it3.663
r_mcangle_it2.419
r_angle_other_deg2.293
r_angle_refined_deg1.681
r_mcbond_it1.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.939
r_dihedral_angle_3_deg12.18
r_dihedral_angle_4_deg9.021
r_dihedral_angle_1_deg5.67
r_scangle_it5.108
r_scbond_it3.663
r_mcangle_it2.419
r_angle_other_deg2.293
r_angle_refined_deg1.681
r_mcbond_it1.668
r_rigid_bond_restr1.66
r_mcbond_other1.288
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2431
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling