X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1M Tris pH=7 1.5M (NH4)2SO4 17% Glycerol
Crystal Properties
Matthews coefficientSolvent content
3.1460.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.54α = 90
b = 69.54β = 90
c = 185.84γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5415

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
11.77433.7799.940.0145430.97204514918
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)
11.7741.83799.910.0526412.0715

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 REPLACEMENTTHROUGHOUT1HYZ1.77433.7742865227699.960.157550.156030.18655RANDOM18.588
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]
0.280.28-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.282
r_dihedral_angle_4_deg15.883
r_dihedral_angle_3_deg11.719
r_dihedral_angle_1_deg6.58
r_long_range_B_refined5.343
r_long_range_B_other5.267
r_scangle_other4.433
r_scbond_it3.112
r_scbond_other3.064
r_mcangle_it2.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.282
r_dihedral_angle_4_deg15.883
r_dihedral_angle_3_deg11.719
r_dihedral_angle_1_deg6.58
r_long_range_B_refined5.343
r_long_range_B_other5.267
r_scangle_other4.433
r_scbond_it3.112
r_scbond_other3.064
r_mcangle_it2.575
r_mcangle_other2.575
r_angle_refined_deg2.394
r_mcbond_it1.826
r_mcbond_other1.793
r_angle_other_deg1.281
r_chiral_restr0.142
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.004
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 Atoms2503
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing