X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310 mM ZnSO4, 100 mM MES and 25% PEG 550 MME
Crystal Properties
Matthews coefficientSolvent content
2.7755.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.32α = 90
b = 44.232β = 90.04
c = 136.187γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-12-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.34090.40.17124.122632-1.5-1.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.3690.60.6953.9

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 REPLACEMENTTHROUGHOUT1SHH3.332.5921544108789.490.228690.224830.30801RANDOM68.129
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]
-30.57-2.55-3.6734.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.764
r_dihedral_angle_3_deg20.3
r_dihedral_angle_4_deg18.152
r_dihedral_angle_1_deg9.545
r_long_range_B_refined9.335
r_long_range_B_other9.335
r_mcangle_it6.864
r_mcangle_other6.864
r_scangle_other6.376
r_mcbond_it4.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.764
r_dihedral_angle_3_deg20.3
r_dihedral_angle_4_deg18.152
r_dihedral_angle_1_deg9.545
r_long_range_B_refined9.335
r_long_range_B_other9.335
r_mcangle_it6.864
r_mcangle_other6.864
r_scangle_other6.376
r_mcbond_it4.387
r_mcbond_other4.387
r_scbond_it4.064
r_scbond_other4.064
r_angle_refined_deg1.818
r_angle_other_deg1.076
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.003
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 Atoms8941
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing