X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DRW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M sodium chloride 0.1 M BIS-TRIS, pH 5.5 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.565α = 90
b = 154.565β = 90
c = 50.483γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.9847.2499.60.188.715.8493701
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)
11.982.199.60.89

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 REPLACEMENTTHROUGHOUT3DRW1.984789122455899.70.1880.1860.224RANDOM25.17
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]
0.160.080.16-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.004
r_dihedral_angle_4_deg14.785
r_dihedral_angle_3_deg14.063
r_dihedral_angle_1_deg6.122
r_angle_refined_deg1.739
r_angle_other_deg1.473
r_chiral_restr0.147
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.004
r_dihedral_angle_4_deg14.785
r_dihedral_angle_3_deg14.063
r_dihedral_angle_1_deg6.122
r_angle_refined_deg1.739
r_angle_other_deg1.473
r_chiral_restr0.147
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.006
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11079
Nucleic Acid Atoms
Solvent Atoms689
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing