X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K3EPDB entry 1K3E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298100 mM Bis-Tris propane, 200 mM MgCl2, 35% PEG 3350, 3.95 mM FOS-choline-9, 5% (v/v) Jeffamine M-600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2745.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.838α = 90
b = 46.832β = 106.39
c = 65.936γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210toroidal mirror2008-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1000NSLSX12C

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
12.495098.50.06413.53.6210664106641154.8
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)
12.492.5894.60.3163.43.58

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 1K3E2.533.411101701017053899.910.216350.214480.25256RANDOM63.824
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]
-2.161.66-0.984.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.567
r_dihedral_angle_3_deg16.972
r_dihedral_angle_4_deg14.049
r_scangle_it7.418
r_dihedral_angle_1_deg6.073
r_scbond_it5.029
r_mcangle_it4.111
r_mcbond_it2.323
r_angle_refined_deg1.371
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.567
r_dihedral_angle_3_deg16.972
r_dihedral_angle_4_deg14.049
r_scangle_it7.418
r_dihedral_angle_1_deg6.073
r_scbond_it5.029
r_mcangle_it4.111
r_mcbond_it2.323
r_angle_refined_deg1.371
r_nbtor_refined0.314
r_symmetry_vdw_refined0.243
r_nbd_refined0.224
r_symmetry_hbond_refined0.221
r_xyhbond_nbd_refined0.15
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2174
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling