X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ELB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7293.150.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.0840.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.785α = 90
b = 100.543β = 117
c = 93.012γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.979531MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.9547.4297.70.1496.22.718418667464
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95298.51.2510.41

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 REPLACEMENTTHROUGHOUT5ELB1.9547.4264017344297.510.189210.186610.23743RANDOM30.418
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]
0.16-0.160.2-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.625
r_dihedral_angle_4_deg29.213
r_dihedral_angle_3_deg15.458
r_dihedral_angle_1_deg8.145
r_long_range_B_refined3.432
r_long_range_B_other3.432
r_angle_refined_deg1.679
r_scangle_other1.656
r_mcangle_it1.52
r_mcangle_other1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.625
r_dihedral_angle_4_deg29.213
r_dihedral_angle_3_deg15.458
r_dihedral_angle_1_deg8.145
r_long_range_B_refined3.432
r_long_range_B_other3.432
r_angle_refined_deg1.679
r_scangle_other1.656
r_mcangle_it1.52
r_mcangle_other1.52
r_scbond_it1.05
r_scbond_other1.05
r_mcbond_it0.956
r_mcbond_other0.956
r_angle_other_deg0.929
r_chiral_restr0.073
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8131
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms290

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing