X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RU4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 mM sodium/potassium phosphate 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9436.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.55α = 90
b = 123.82β = 90
c = 138.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4839.6599.90.99913.47221195
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5199.90.7362.6

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 REPLACEMENTTHROUGHOUT1RU41.4839.652102261086999.880.128830.126760.1689RANDOM16.158
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]
-0.150.48-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.521
r_sphericity_free22.376
r_dihedral_angle_3_deg11.414
r_dihedral_angle_4_deg10.379
r_sphericity_bonded7.368
r_dihedral_angle_1_deg7.121
r_long_range_B_refined3.093
r_long_range_B_other2.828
r_scangle_other2.454
r_scbond_it2.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.521
r_sphericity_free22.376
r_dihedral_angle_3_deg11.414
r_dihedral_angle_4_deg10.379
r_sphericity_bonded7.368
r_dihedral_angle_1_deg7.121
r_long_range_B_refined3.093
r_long_range_B_other2.828
r_scangle_other2.454
r_scbond_it2.103
r_scbond_other2.091
r_rigid_bond_restr1.851
r_mcangle_it1.834
r_mcangle_other1.834
r_angle_refined_deg1.54
r_mcbond_it1.449
r_mcbond_other1.448
r_angle_other_deg0.986
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9800
Nucleic Acid Atoms
Solvent Atoms1519
Heterogen Atoms18

Software

Software
Software NamePurpose
xia2data reduction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
REFMACrefinement