X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.15100 mM BIS-TRIS, 1.8 M Ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.0941.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.48α = 90
b = 72.97β = 114.3
c = 86.99γ = 90
Symmetry
Space GroupP 1 21 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-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3533.196.50.0830.050.9959.73.7193517
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4294.40.5190.3080.7593.83.8

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 REPLACEMENTTHROUGHOUT1QOK1.3533.1191623186896.290.136330.135870.18397RANDOM15.295
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]
-0.09-0.050.36-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.718
r_sphericity_free22.205
r_dihedral_angle_4_deg19.953
r_dihedral_angle_3_deg11.091
r_sphericity_bonded8.975
r_dihedral_angle_1_deg7.84
r_rigid_bond_restr4.551
r_long_range_B_refined3.648
r_long_range_B_other3.441
r_scangle_other3.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.718
r_sphericity_free22.205
r_dihedral_angle_4_deg19.953
r_dihedral_angle_3_deg11.091
r_sphericity_bonded8.975
r_dihedral_angle_1_deg7.84
r_rigid_bond_restr4.551
r_long_range_B_refined3.648
r_long_range_B_other3.441
r_scangle_other3.258
r_scbond_it2.872
r_scbond_other2.872
r_mcangle_it2.611
r_mcangle_other2.611
r_mcbond_it2.288
r_mcbond_other2.288
r_angle_refined_deg1.758
r_angle_other_deg0.938
r_chiral_restr0.116
r_bond_refined_d0.014
r_gen_planes_refined0.01
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7395
Nucleic Acid Atoms
Solvent Atoms868
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing