X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OKOPDB ENTRY 1OKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5SOLUTION 20 OF THE CSSI SCREEN 8% PEG 20K, 8% PEG550MME, 100 MM TRIS 8.5 AND 0.2 M LI2SO4
Crystal Properties
Matthews coefficientSolvent content
2.6353.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.876α = 90
b = 66.259β = 90
c = 159.427γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESERACH2013-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.6548.471000.0422.95.4658072
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)
11.651.681000.5135.5

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 1OKO1.6548.4762390333499.910.156650.155250.18362RANDOM26.643
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]
-0.752.17-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.637
r_dihedral_angle_3_deg10.707
r_dihedral_angle_1_deg6.041
r_dihedral_angle_4_deg5.514
r_scbond_it2.17
r_mcangle_it1.809
r_angle_refined_deg1.725
r_mcbond_it1.201
r_mcbond_other1.2
r_angle_other_deg0.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.637
r_dihedral_angle_3_deg10.707
r_dihedral_angle_1_deg6.041
r_dihedral_angle_4_deg5.514
r_scbond_it2.17
r_mcangle_it1.809
r_angle_refined_deg1.725
r_mcbond_it1.201
r_mcbond_other1.2
r_angle_other_deg0.783
r_symmetry_vdw_refined0.28
r_nbd_refined0.241
r_nbd_other0.181
r_nbtor_refined0.178
r_symmetry_vdw_other0.178
r_metal_ion_refined0.154
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.106
r_chiral_restr0.105
r_nbtor_other0.081
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3614
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing