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, 200 mM calcium acetate, 18% PEG-8000, 4 mM MgCl2, 50 uM CTP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.166α = 90
b = 42.157β = 93.66
c = 106.809γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2006-07-29MSINGLE 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
12.245.8998.20.117.43.4736623
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)
2.22.2896.80.5122.13.523555

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 2IKF2.245.8836610188398.240.2340.2320.281test set taken from 2IKF41.655
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]
0.080.16-0.05-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.736
r_dihedral_angle_3_deg19.526
r_dihedral_angle_4_deg14.288
r_dihedral_angle_1_deg6.441
r_scangle_it2.632
r_scbond_it1.728
r_angle_refined_deg1.566
r_mcangle_it1.299
r_mcbond_it0.737
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.736
r_dihedral_angle_3_deg19.526
r_dihedral_angle_4_deg14.288
r_dihedral_angle_1_deg6.441
r_scangle_it2.632
r_scbond_it1.728
r_angle_refined_deg1.566
r_mcangle_it1.299
r_mcbond_it0.737
r_nbtor_refined0.303
r_symmetry_vdw_refined0.208
r_nbd_refined0.206
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.168
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5108
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms30

Software

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