X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XYS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.45 M ammonium phosphate monobasic 2 % glycerol 2 % IPA
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.781α = 90
b = 131.999β = 103.15
c = 130.655γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDRIGAKU SATURN 944+Varimax Cu-VHF2016-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54157

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
12.225.299.90.1150.9938.86.817607027.2
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)
12.22.2499.90.6390.6753.36.7

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 REPLACEMENTTHROUGHOUT2xys2.225.2167118865399.710.204440.202860.23515RANDOM34.896
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]
-1.93-0.241.530.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.957
r_dihedral_angle_4_deg15.259
r_long_range_B_other13.003
r_long_range_B_refined12.976
r_scangle_other12.036
r_dihedral_angle_3_deg11.99
r_scbond_it9.273
r_scbond_other9.272
r_dihedral_angle_1_deg8.205
r_mcangle_it6.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.957
r_dihedral_angle_4_deg15.259
r_long_range_B_other13.003
r_long_range_B_refined12.976
r_scangle_other12.036
r_dihedral_angle_3_deg11.99
r_scbond_it9.273
r_scbond_other9.272
r_dihedral_angle_1_deg8.205
r_mcangle_it6.849
r_mcangle_other6.849
r_mcbond_it5.902
r_mcbond_other5.902
r_angle_refined_deg1.451
r_angle_other_deg0.972
r_chiral_restr0.089
r_bond_refined_d0.009
r_bond_other_d0.008
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16502
Nucleic Acid Atoms
Solvent Atoms1801
Heterogen Atoms568

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing