X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E8M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.88α = 90
b = 70.89β = 94.91
c = 78.23γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6338.4299.511.7461989
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)
11.641.670.61

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 REPLACEMENTTHROUGHOUT5e8m1.6338.4257972312599.790.167330.165710.19677taken from apo structure29.499
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]
1.020.57-0.28-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.29
r_dihedral_angle_4_deg17.469
r_dihedral_angle_3_deg12.524
r_long_range_B_refined6.638
r_long_range_B_other6.637
r_dihedral_angle_1_deg6.336
r_scangle_other4.553
r_mcangle_it3.328
r_mcangle_other3.327
r_scbond_it2.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.29
r_dihedral_angle_4_deg17.469
r_dihedral_angle_3_deg12.524
r_long_range_B_refined6.638
r_long_range_B_other6.637
r_dihedral_angle_1_deg6.336
r_scangle_other4.553
r_mcangle_it3.328
r_mcangle_other3.327
r_scbond_it2.905
r_scbond_other2.904
r_mcbond_it2.185
r_mcbond_other2.185
r_angle_refined_deg1.671
r_angle_other_deg0.974
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3643
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling