2R2E

Crystal structure of S25-2 Fab in complex with Kdo analogues


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8300PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.11α = 90
b = 81.17β = 90
c = 132.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.419.8795.50.05912.34.1617962
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)
2.42.4998.20.21343.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.419.871703792195.480.246730.243390.30618RANDOM35.033
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.551
r_dihedral_angle_4_deg19.148
r_dihedral_angle_3_deg15.982
r_dihedral_angle_1_deg7.118
r_scangle_it2.098
r_angle_refined_deg1.456
r_scbond_it1.407
r_mcangle_it1.164
r_mcbond_it0.678
r_symmetry_hbond_refined0.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.551
r_dihedral_angle_4_deg19.148
r_dihedral_angle_3_deg15.982
r_dihedral_angle_1_deg7.118
r_scangle_it2.098
r_angle_refined_deg1.456
r_scbond_it1.407
r_mcangle_it1.164
r_mcbond_it0.678
r_symmetry_hbond_refined0.404
r_nbtor_refined0.3
r_symmetry_vdw_refined0.23
r_nbd_refined0.209
r_xyhbond_nbd_refined0.154
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3387
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms19

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction