X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.3 M sodium acetate, 0.1 M Tris 10% PEG 8000 (w/v) + 10% PEG 1000 (w/v), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6253.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.88α = 90
b = 133.88β = 90
c = 73.02γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.97DiamondI04-1

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
12.0429.431000.0813106431064
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)
12.042.0881000.4321.91

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2ZBY2.0429.43294962949615681000.197530.1950.24653RANDOM26.702
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]
-0.14-0.07-0.140.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.788
r_dihedral_angle_4_deg20.264
r_dihedral_angle_3_deg15.712
r_dihedral_angle_1_deg6.539
r_scangle_it4.683
r_scbond_it3.108
r_mcangle_it2.049
r_angle_refined_deg1.908
r_mcbond_it1.155
r_angle_other_deg1.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.788
r_dihedral_angle_4_deg20.264
r_dihedral_angle_3_deg15.712
r_dihedral_angle_1_deg6.539
r_scangle_it4.683
r_scbond_it3.108
r_mcangle_it2.049
r_angle_refined_deg1.908
r_mcbond_it1.155
r_angle_other_deg1.069
r_mcbond_other0.328
r_chiral_restr0.133
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d0.006
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_mcangle_other
r_scbond_other
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 Atoms2987
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms43

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling