X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52941.6 M tri-sodium citrate, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.2361.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.608α = 90
b = 102.14β = 90
c = 116.508γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
12.241.7799.20.07712.84.344268
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)
12.22.2799.70.91124.4

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 REPLACEMENTTHROUGHOUT1IJY2.24042000222798.960.1790.17670.2227RANDOM46.189
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]
-0.331.19-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.95
r_dihedral_angle_2_deg34.718
r_dihedral_angle_3_deg17.597
r_dihedral_angle_4_deg11.673
r_sphericity_bonded10.712
r_dihedral_angle_1_deg6.368
r_mcangle_it2.903
r_mcbond_it2.125
r_mcbond_other2.092
r_rigid_bond_restr1.523
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.95
r_dihedral_angle_2_deg34.718
r_dihedral_angle_3_deg17.597
r_dihedral_angle_4_deg11.673
r_sphericity_bonded10.712
r_dihedral_angle_1_deg6.368
r_mcangle_it2.903
r_mcbond_it2.125
r_mcbond_other2.092
r_rigid_bond_restr1.523
r_angle_refined_deg1.279
r_angle_other_deg0.788
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3866
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms70

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement