4FRD

Crystal Structure of ABBA+UDP+Gal at pH 9.0 with MPD as the cryoprotectant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.52α = 90
b = 149.28β = 90
c = 79.75γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC BLUE MIRRORS2008-12-04MSINGLE 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
11.552097.80.03617.54.4344858
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)
11.551.6199.50.3193.33.74505

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 REPLACEMENTTHROUGHOUT1LZ71.552044856226997.690.17990.17810.2142RANDOM25.1813
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]
-0.680.310.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_dihedral_angle_4_deg19.404
r_dihedral_angle_3_deg14.402
r_dihedral_angle_1_deg6.685
r_angle_refined_deg2.297
r_angle_other_deg1.168
r_chiral_restr0.148
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_dihedral_angle_4_deg19.404
r_dihedral_angle_3_deg14.402
r_dihedral_angle_1_deg6.685
r_angle_refined_deg2.297
r_angle_other_deg1.168
r_chiral_restr0.148
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2320
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms38

Software

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