X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SOA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.15100mM TRIS-HCl, 200mM sodium citrate, 30% PEG-400, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.0459.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.86α = 90
b = 74.86β = 90
c = 74.69γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
11.632.499.80.09110.2532338
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)
11.61.6998.70.6172.44.9

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 REPLACEMENTTHROUGHOUT1SOA1.632.430987132499.80.145880.144840.17192RANDOM16.74
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]
-0.16-0.08-0.160.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.201
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg14.607
r_long_range_B_refined6.879
r_long_range_B_other6.502
r_dihedral_angle_1_deg6.304
r_scangle_other4.588
r_scbond_it2.906
r_scbond_other2.904
r_mcangle_other2.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.201
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg14.607
r_long_range_B_refined6.879
r_long_range_B_other6.502
r_dihedral_angle_1_deg6.304
r_scangle_other4.588
r_scbond_it2.906
r_scbond_other2.904
r_mcangle_other2.518
r_mcangle_it2.51
r_angle_refined_deg2.026
r_mcbond_it1.598
r_mcbond_other1.573
r_angle_other_deg0.913
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
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 Atoms1376
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing