X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DY6PDB entry 1DY6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529120% PEG 6000, 0.1 M KSCN, 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7755.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 91.3β = 112.6
c = 73.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77IMAGE PLATEMAR scanner 345 mm platemirror 1, double crystal, mirror 22006-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97900ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.619.7696.50.0521.543.38668014.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.795.20.13711.68314100

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 1DY61.619.768234743351000.188750.187580.2108RANDOM10.889
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]
-0.02-0.220.36-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.886
r_dihedral_angle_4_deg15.125
r_dihedral_angle_3_deg11.953
r_dihedral_angle_1_deg5.478
r_sphericity_free4.654
r_scangle_it3.059
r_sphericity_bonded2.353
r_scbond_it2.125
r_mcangle_it1.375
r_angle_refined_deg1.255
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.886
r_dihedral_angle_4_deg15.125
r_dihedral_angle_3_deg11.953
r_dihedral_angle_1_deg5.478
r_sphericity_free4.654
r_scangle_it3.059
r_sphericity_bonded2.353
r_scbond_it2.125
r_mcangle_it1.375
r_angle_refined_deg1.255
r_rigid_bond_restr1.185
r_mcbond_it0.936
r_nbtor_refined0.304
r_nbd_refined0.232
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.096
r_chiral_restr0.084
r_symmetry_hbond_refined0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3953
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Xnemodata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing