X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YP1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.1512% PEG 20000, 0.1M MES pH6.5, 20% Glycerol, 5.5mM DiprotinA(IPI)
Crystal Properties
Matthews coefficientSolvent content
2.8757.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.88α = 90
b = 120.12β = 90
c = 262.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702012-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9788Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.4360.0697.30.0870.0940.0340.99814.36.713919439.076
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.4781.20.4320.5150.2710.78723.3

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 REPLACEMENTTHROUGHOUT5YP12.4440130819683597.40.240660.238260.28627RANDOM43.448
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]
-2.141.860.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.745
r_dihedral_angle_4_deg17.65
r_dihedral_angle_3_deg17.379
r_dihedral_angle_1_deg8.032
r_long_range_B_other6.574
r_long_range_B_refined6.572
r_mcangle_it4.761
r_mcangle_other4.761
r_scangle_other4.106
r_mcbond_it3.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.745
r_dihedral_angle_4_deg17.65
r_dihedral_angle_3_deg17.379
r_dihedral_angle_1_deg8.032
r_long_range_B_other6.574
r_long_range_B_refined6.572
r_mcangle_it4.761
r_mcangle_other4.761
r_scangle_other4.106
r_mcbond_it3.139
r_mcbond_other3.139
r_scbond_it2.717
r_scbond_other2.717
r_angle_refined_deg1.772
r_angle_other_deg1.065
r_chiral_restr0.095
r_bond_refined_d0.014
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
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 Atoms22640
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing