X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IKFPDB entry 2IKF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277100 mM sodium cacodylate pH 6.5, 200 mM magnesium chloride, 18% PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.142α = 90
b = 41.659β = 96.46
c = 104.286γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979SSRLBL9-1

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
12.441.299.50.1784.93.4826868
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)
2.42.4999.80.50923.562665

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 2IKF2.441.226857139399.510.2340.230.301RANDOM36.886
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]
0.04-0.07-0.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.299
r_dihedral_angle_3_deg19.412
r_dihedral_angle_4_deg18.144
r_dihedral_angle_1_deg5.775
r_scangle_it2.541
r_scbond_it1.591
r_angle_refined_deg1.422
r_mcangle_it1.292
r_mcbond_it0.73
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.299
r_dihedral_angle_3_deg19.412
r_dihedral_angle_4_deg18.144
r_dihedral_angle_1_deg5.775
r_scangle_it2.541
r_scbond_it1.591
r_angle_refined_deg1.422
r_mcangle_it1.292
r_mcbond_it0.73
r_nbtor_refined0.309
r_symmetry_vdw_refined0.259
r_nbd_refined0.221
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.185
r_metal_ion_refined0.108
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4645
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms58

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
d*TREKdata reduction