4M7J

Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T2QPDB ENTRY 1T2Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.2M potassium chloride, 0.05M HEPES, 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5150.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.464α = 90
b = 74.464β = 90
c = 149.893γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDVertical focusing mirror2011-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9794CLSI08ID-1

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
11.952599.90.0641113.7359672.2
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)
11.952.021000.55612.83558

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 1T2Q1.9524.4535920179399.810.21340.21170.247RANDOM63.074
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]
1.571.571.57-5.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.804
r_dihedral_angle_4_deg17.261
r_dihedral_angle_3_deg16.123
r_dihedral_angle_1_deg7.313
r_mcangle_it2.483
r_mcbond_it1.635
r_mcbond_other1.633
r_angle_refined_deg1.482
r_angle_other_deg0.842
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.804
r_dihedral_angle_4_deg17.261
r_dihedral_angle_3_deg16.123
r_dihedral_angle_1_deg7.313
r_mcangle_it2.483
r_mcbond_it1.635
r_mcbond_other1.633
r_angle_refined_deg1.482
r_angle_other_deg0.842
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3368
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms71

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Macromoleculardata collection