X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EEP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris-Hcl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 0 or 15 mM CoCl2
Crystal Properties
Matthews coefficientSolvent content
2.0539.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.5α = 90
b = 40.5β = 90
c = 133.76γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9763ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
128099.80.1760.99712.78.28116
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)
122.11001.060.7352.58.7

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 REPLACEMENTTHROUGHOUT4eep238.76773438499.670.18250.179730.2402RANDOM34.467
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]
-0.02-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.269
r_dihedral_angle_1_deg23.658
r_dihedral_angle_4_deg19.938
r_dihedral_angle_3_deg15.467
r_long_range_B_refined7.621
r_long_range_B_other7.562
r_scangle_other4.005
r_mcangle_it3.588
r_mcangle_other3.585
r_scbond_it2.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.269
r_dihedral_angle_1_deg23.658
r_dihedral_angle_4_deg19.938
r_dihedral_angle_3_deg15.467
r_long_range_B_refined7.621
r_long_range_B_other7.562
r_scangle_other4.005
r_mcangle_it3.588
r_mcangle_other3.585
r_scbond_it2.418
r_scbond_other2.416
r_mcbond_it2.298
r_mcbond_other2.298
r_angle_refined_deg1.554
r_angle_other_deg0.898
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms913
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms51

Software

Software
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
Cootmodel building