X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.99α = 90
b = 299.93β = 113.23
c = 145.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.75098.70.07111.43.1274527
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)
12.72.899.70.4922.1

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 REPLACEMENTTHROUGHOUT5CZ42.7152745271444998.210.176730.175170.20619RANDOM66.927
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]
1.75-1.07-3.592.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_sphericity_free32.317
r_sphericity_bonded19.379
r_dihedral_angle_3_deg15.412
r_dihedral_angle_4_deg15.189
r_dihedral_angle_1_deg5.75
r_long_range_B_refined4.8
r_long_range_B_other4.784
r_mcangle_it4.196
r_mcangle_other4.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_sphericity_free32.317
r_sphericity_bonded19.379
r_dihedral_angle_3_deg15.412
r_dihedral_angle_4_deg15.189
r_dihedral_angle_1_deg5.75
r_long_range_B_refined4.8
r_long_range_B_other4.784
r_mcangle_it4.196
r_mcangle_other4.196
r_scangle_other3.864
r_mcbond_it3.079
r_mcbond_other3.079
r_scbond_it3.003
r_scbond_other3.003
r_rigid_bond_restr2.61
r_angle_refined_deg1.164
r_angle_other_deg0.889
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms49304
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms168

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement