X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YLAPDB entries 1YLA and 1A3S
experimental modelPDB 1A3SPDB entries 1YLA and 1A3S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.0759.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.874α = 85.05
b = 68.498β = 80.85
c = 91.277γ = 75.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.91841CHESSA1

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
12.63093.30.05113.91.92765127651-3
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)
12.62.6470.80.2932.171.71028

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 1YLA and 1A3S2.6302765126281139892.920.231050.227750.29091RANDOM34.036
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]
-2.310.791.94-2.91-1.174.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.074
r_dihedral_angle_3_deg20.218
r_dihedral_angle_4_deg14.615
r_dihedral_angle_1_deg5.437
r_scangle_it1.693
r_angle_refined_deg1.624
r_scbond_it1.068
r_mcangle_it0.636
r_mcbond_it0.4
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.074
r_dihedral_angle_3_deg20.218
r_dihedral_angle_4_deg14.615
r_dihedral_angle_1_deg5.437
r_scangle_it1.693
r_angle_refined_deg1.624
r_scbond_it1.068
r_mcangle_it0.636
r_mcbond_it0.4
r_nbtor_refined0.302
r_symmetry_vdw_refined0.227
r_nbd_refined0.208
r_xyhbond_nbd_refined0.151
r_chiral_restr0.1
r_symmetry_hbond_refined0.091
r_bond_refined_d0.016
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5628
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing