X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O5N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
3.3463.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.334α = 90
b = 100.333β = 90
c = 385.597γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rpim 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
11.855098.70.090.02143.317.56392928
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9199.50.950.240.932.716

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 REPLACEMENTTHROUGHOUT4O5N1.855060707322198.420.167660.166760.18477RANDOM40.166
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]
0.830.410.83-2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg18.87
r_dihedral_angle_3_deg13.864
r_long_range_B_refined6.451
r_long_range_B_other6.129
r_dihedral_angle_1_deg6.06
r_scangle_other2.929
r_scbond_it1.739
r_scbond_other1.739
r_mcangle_it1.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg18.87
r_dihedral_angle_3_deg13.864
r_long_range_B_refined6.451
r_long_range_B_other6.129
r_dihedral_angle_1_deg6.06
r_scangle_other2.929
r_scbond_it1.739
r_scbond_other1.739
r_mcangle_it1.661
r_mcangle_other1.66
r_angle_refined_deg1.474
r_mcbond_it1.024
r_mcbond_other1.024
r_angle_other_deg0.933
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3869
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing