X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YTO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.5M Sodium Citrate, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.867.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.367α = 90
b = 203.692β = 90
c = 144.211γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.5201000.07919.76.58375039.1
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)
12.52.51000.54825.7

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 REPLACEMENTTHROUGHOUT5YTO2.52079255417299.730.166110.163420.23712RANDOM42.145
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]
1.30.48-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.504
r_dihedral_angle_4_deg22.129
r_dihedral_angle_3_deg18.763
r_long_range_B_refined7.536
r_dihedral_angle_1_deg7.353
r_scbond_it5.12
r_mcangle_it4.632
r_mcbond_it3.401
r_angle_refined_deg2.319
r_chiral_restr0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.504
r_dihedral_angle_4_deg22.129
r_dihedral_angle_3_deg18.763
r_long_range_B_refined7.536
r_dihedral_angle_1_deg7.353
r_scbond_it5.12
r_mcangle_it4.632
r_mcbond_it3.401
r_angle_refined_deg2.319
r_chiral_restr0.147
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms10936
Nucleic Acid Atoms
Solvent Atoms1234
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing