X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherour previous model of S1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52910.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.1743.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.184α = 107.37
b = 48.595β = 90.13
c = 65.469γ = 105.72
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0PETRA III, EMBL c/o DESYP13 (MX1)

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
11.543.0588.20.069.21.8688285.8
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)
11.51.5354.60.1873.81.8

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 REPLACEMENTTHROUGHOUTour previous model of S11.543.0568827336488.220.149630.148770.17736Random selection13.322
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]
-1.070.180.110.970.01-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_3_deg11.398
r_dihedral_angle_4_deg8.639
r_dihedral_angle_1_deg5.715
r_long_range_B_refined4.825
r_long_range_B_other4.135
r_scangle_other2.179
r_angle_refined_deg1.647
r_scbond_it1.48
r_scbond_other1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_3_deg11.398
r_dihedral_angle_4_deg8.639
r_dihedral_angle_1_deg5.715
r_long_range_B_refined4.825
r_long_range_B_other4.135
r_scangle_other2.179
r_angle_refined_deg1.647
r_scbond_it1.48
r_scbond_other1.48
r_angle_other_deg1.376
r_mcangle_it1.354
r_mcangle_other1.354
r_mcbond_it0.904
r_mcbond_other0.899
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.004
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 Atoms4084
Nucleic Acid Atoms
Solvent Atoms871
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building