X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KSGPDB ENTRY 1KSG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92930.2M MgCl2, 20% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.663α = 90
b = 45.165β = 90
c = 175.879γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 42007-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.35099.40.1610.16111.45.3585358181187.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.33.4297.30.7590.7592.45.3565

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KSG3.340.185538552029799.660.25530.25530.253270.29443RANDOM76.322
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]
-4.666.28-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.892
r_dihedral_angle_3_deg19.162
r_dihedral_angle_4_deg13.718
r_dihedral_angle_1_deg6.036
r_mcangle_it1.972
r_scangle_it1.896
r_rigid_bond_restr1.638
r_scbond_it1.464
r_mcbond_it1.13
r_angle_refined_deg1.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.892
r_dihedral_angle_3_deg19.162
r_dihedral_angle_4_deg13.718
r_dihedral_angle_1_deg6.036
r_mcangle_it1.972
r_scangle_it1.896
r_rigid_bond_restr1.638
r_scbond_it1.464
r_mcbond_it1.13
r_angle_refined_deg1.074
r_symmetry_hbond_refined0.69
r_sphericity_free0.534
r_sphericity_bonded0.471
r_nbtor_refined0.303
r_symmetry_vdw_refined0.256
r_nbd_refined0.218
r_xyhbond_nbd_refined0.147
r_metal_ion_refined0.135
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2526
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms33

Software

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