X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DK5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277100mM Hepes (pH 7.5), 1mM DTT, 8% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9658.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.28α = 90
b = 76.28β = 90
c = 277.23γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHVarimax optics2009-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
11.9847.8299.5941778
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.981.9999.59

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 REPLACEMENTTHROUGHOUT3DK51.9847.8241778104899.590.160.15890.2005RANDOM31.3647
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg14.942
r_dihedral_angle_1_deg7.073
r_scangle_it5.438
r_scbond_it3.483
r_angle_refined_deg2.157
r_mcangle_it2.117
r_mcbond_it1.244
r_chiral_restr0.255
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg14.942
r_dihedral_angle_1_deg7.073
r_scangle_it5.438
r_scbond_it3.483
r_angle_refined_deg2.157
r_mcangle_it2.117
r_mcbond_it1.244
r_chiral_restr0.255
r_bond_refined_d0.027
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3428
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms74

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASESphasing