2R23

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q9Q 

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
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.64α = 90
b = 81.38β = 90
c = 131.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2007-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0021.54

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
11.6519.995.80.04413.54.4257118
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)
11.651.7196.30.3653.13.715670

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 REPLACEMENTTHROUGHOUT1Q9Q1.652057114288995.820.230.2280.264RANDOM30.178
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]
2.28-1.48-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.683
r_dihedral_angle_4_deg19.345
r_dihedral_angle_3_deg14.189
r_dihedral_angle_1_deg6.757
r_scangle_it3.34
r_scbond_it2.373
r_mcangle_it1.666
r_angle_refined_deg1.567
r_mcbond_it1.013
r_symmetry_hbond_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.683
r_dihedral_angle_4_deg19.345
r_dihedral_angle_3_deg14.189
r_dihedral_angle_1_deg6.757
r_scangle_it3.34
r_scbond_it2.373
r_mcangle_it1.666
r_angle_refined_deg1.567
r_mcbond_it1.013
r_symmetry_hbond_refined0.316
r_nbtor_refined0.302
r_nbd_refined0.23
r_symmetry_vdw_refined0.216
r_symmetry_metal_ion_refined0.206
r_xyhbond_nbd_refined0.127
r_chiral_restr0.109
r_metal_ion_refined0.072
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3380
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms37

Software

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