3SXE

Crystal structure of AAAA+UDP+Gal with Glycerol as the cryoprotectant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ0PDB ENTRY 1LZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP72981% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM MnCl2, with 30% glycerol as the cryoprotectant, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.55α = 90
b = 149.63β = 90
c = 79.76γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC BLUE MIRRORS2008-05-22MSINGLE 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
11.4974.74496.90.04315.54.3350161
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)
11.491.5497.80.36433.53

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 1LZ01.492047595256396.930.191730.190270.21938RANDOM21.006
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]
-0.450.180.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.863
r_dihedral_angle_4_deg16.882
r_dihedral_angle_3_deg13.336
r_dihedral_angle_1_deg6.499
r_scangle_it5.089
r_scbond_it3.383
r_mcangle_it2.26
r_angle_refined_deg2.256
r_mcbond_it1.396
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.863
r_dihedral_angle_4_deg16.882
r_dihedral_angle_3_deg13.336
r_dihedral_angle_1_deg6.499
r_scangle_it5.089
r_scbond_it3.383
r_mcangle_it2.26
r_angle_refined_deg2.256
r_mcbond_it1.396
r_chiral_restr0.158
r_bond_refined_d0.029
r_gen_planes_refined0.014
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2412
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms50

Software

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