X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5SOLUTION 15 OF THE CSSI SCREEN 10 % PEG 8K, 10% PEG 1K, 100 MM TRIS 8.5 AND 200 MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.652.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.666α = 90
b = 65.393β = 90
c = 159.869γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2013-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.5739.9799.90.0719.27.6751102
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)
11.571.699.40.382.94

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 1OKO1.5739.9771247377799.850.164710.163310.19138RANDOM35.32
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]
-0.972.72-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.155
r_dihedral_angle_3_deg11.919
r_dihedral_angle_4_deg6.78
r_dihedral_angle_1_deg5.9
r_scbond_it2.219
r_mcangle_it1.89
r_angle_refined_deg1.763
r_mcbond_it1.339
r_mcbond_other1.337
r_angle_other_deg0.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.155
r_dihedral_angle_3_deg11.919
r_dihedral_angle_4_deg6.78
r_dihedral_angle_1_deg5.9
r_scbond_it2.219
r_mcangle_it1.89
r_angle_refined_deg1.763
r_mcbond_it1.339
r_mcbond_other1.337
r_angle_other_deg0.795
r_nbd_refined0.243
r_symmetry_vdw_refined0.24
r_symmetry_vdw_other0.214
r_nbtor_refined0.178
r_nbd_other0.177
r_metal_ion_refined0.115
r_chiral_restr0.105
r_xyhbond_nbd_refined0.104
r_nbtor_other0.081
r_symmetry_hbond_refined0.039
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_xyhbond_nbd_other0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3619
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing