X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5277Na cacodyrate, Mg(NO3)2, PEG 4000, GalNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4149.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.861α = 105.2
b = 111.658β = 90.48
c = 118.66γ = 107.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 42007-03-11MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152006-11-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A
2SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A0.97934, 0.97974, 0.96450Photon FactoryBL-5A

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
1,21.950970.05721.0662.664066124343523.6
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)
1,21.91.97960.2323.52.624136

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.944.812434281225496.70.1630.1610.204RANDOM28.094
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]
0.010.070.030.08-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_4_deg17.628
r_dihedral_angle_3_deg13.579
r_dihedral_angle_1_deg5.9
r_scangle_it3.083
r_scbond_it1.993
r_angle_refined_deg1.368
r_mcangle_it1.24
r_mcbond_it0.704
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_4_deg17.628
r_dihedral_angle_3_deg13.579
r_dihedral_angle_1_deg5.9
r_scangle_it3.083
r_scbond_it1.993
r_angle_refined_deg1.368
r_mcangle_it1.24
r_mcbond_it0.704
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23573
Nucleic Acid Atoms
Solvent Atoms3114
Heterogen Atoms124

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing