X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VTKPDB entry 1VTK with unconserved residues modified to alanine

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298Ammonium sulfate, MES, Dioxane , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7354.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.301α = 90
b = 121.014β = 90
c = 118.808γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.147461

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 1VTK with unconserved residues modified to alanine2.129.74141541415454196.780.188860.188860.184180.23175RANDOM28.256
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]
1.48-0.42-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.453
r_scangle_it3.04
r_scbond_it1.953
r_angle_refined_deg1.343
r_mcangle_it1.329
r_mcbond_it0.718
r_nbd_refined0.207
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.453
r_scangle_it3.04
r_scbond_it1.953
r_angle_refined_deg1.343
r_mcangle_it1.329
r_mcbond_it0.718
r_nbd_refined0.207
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.143
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5009
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
XSCALEdata scaling
MOLREPphasing