X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SI9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% (w/v) PEG6000 200 mM lithium acetate 100 mM Bis-Tris-HCl, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.9335.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.446α = 90
b = 88.567β = 105.99
c = 104.574γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.10Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)CC (Half)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
12.8100.5399.30.0440.0480.0210.99919.25.3196401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.95990.1970.2170.0890.9867.75.6

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 REPLACEMENTTHROUGHOUT1SI92.8100.5334927189299.110.211270.207480.27877RANDOM63.358
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]
2.611.393.67-6.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.372
r_dihedral_angle_3_deg19.482
r_dihedral_angle_4_deg15.009
r_long_range_B_refined9.119
r_long_range_B_other9.119
r_dihedral_angle_1_deg8.264
r_mcangle_it6.69
r_mcangle_other6.689
r_scangle_other5.972
r_mcbond_it4.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.372
r_dihedral_angle_3_deg19.482
r_dihedral_angle_4_deg15.009
r_long_range_B_refined9.119
r_long_range_B_other9.119
r_dihedral_angle_1_deg8.264
r_mcangle_it6.69
r_mcangle_other6.689
r_scangle_other5.972
r_mcbond_it4.216
r_mcbond_other4.213
r_scbond_it3.704
r_scbond_other3.704
r_angle_refined_deg1.581
r_angle_other_deg1.023
r_chiral_restr0.104
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10523
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing