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
3.1360.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.43α = 90
b = 75.43β = 90
c = 75.89γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-11-04MSINGLE 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)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
11.4533.899.90.0730.99814.36.944624
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.531000.8380.63425.7

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 REPLACEMENTTHROUGHOUT1SOA1.4533.843288130299.870.133870.133080.16024RANDOM23.715
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]
0.110.060.11-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_sphericity_free31.93
r_dihedral_angle_4_deg17.67
r_sphericity_bonded15.458
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg6.218
r_scangle_other5.723
r_long_range_B_refined5.16
r_scbond_it5.138
r_scbond_other5.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_sphericity_free31.93
r_dihedral_angle_4_deg17.67
r_sphericity_bonded15.458
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg6.218
r_scangle_other5.723
r_long_range_B_refined5.16
r_scbond_it5.138
r_scbond_other5.138
r_long_range_B_other4.867
r_rigid_bond_restr4.576
r_mcangle_other3.161
r_mcangle_it3.144
r_mcbond_it2.812
r_mcbond_other2.737
r_angle_refined_deg1.82
r_angle_other_deg0.921
r_chiral_restr0.112
r_bond_refined_d0.016
r_gen_planes_refined0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1376
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing