X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4POQPDB ENTRY 4POQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.1529320% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactose for 25 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.01α = 90
b = 180.4β = 90
c = 199.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-Fmirrors2013-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
12.09133.85598.970.158.363.15204785206909-3-329.35
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)
12.092.1497.880.781.922.9414851

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4POQ2.09133.8552047851945661021998.890.179440.179440.177510.2157RANDOM27.79
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]
0.56-0.37-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.774
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg13.014
r_dihedral_angle_1_deg6.316
r_long_range_B_refined6.135
r_angle_refined_deg1.234
r_mcangle_it1.229
r_scbond_it1.136
r_mcbond_it0.692
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.774
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg13.014
r_dihedral_angle_1_deg6.316
r_long_range_B_refined6.135
r_angle_refined_deg1.234
r_mcangle_it1.229
r_scbond_it1.136
r_mcbond_it0.692
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
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_it
r_scangle_other
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 Atoms20577
Nucleic Acid Atoms
Solvent Atoms2364
Heterogen Atoms569

Software

Software
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling