X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KO3PDB ENTRY 1KO3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.55 M AMMONIUM CITRATE TRIBASIC PH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.39α = 90
b = 46.22β = 105.24
c = 105.99γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.947.398.60.18.923.65228326.59
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)
11.9295.70.442.593.3

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 1KO31.947.34966726151000.2020.20.254RANDOM26.52
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]
1.67-0.4-1.02-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.772
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg16.411
r_sphericity_free7.259
r_dihedral_angle_1_deg6.337
r_sphericity_bonded3.975
r_scangle_it3.362
r_scbond_it2.278
r_mcangle_it1.579
r_rigid_bond_restr1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.772
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg16.411
r_sphericity_free7.259
r_dihedral_angle_1_deg6.337
r_sphericity_bonded3.975
r_scangle_it3.362
r_scbond_it2.278
r_mcangle_it1.579
r_rigid_bond_restr1.48
r_angle_refined_deg1.424
r_mcbond_it1.023
r_nbtor_refined0.302
r_symmetry_hbond_refined0.231
r_symmetry_vdw_refined0.225
r_nbd_refined0.192
r_xyhbond_nbd_refined0.159
r_chiral_restr0.099
r_metal_ion_refined0.078
r_bond_refined_d0.015
r_gen_planes_refined0.006
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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3454
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing