6GHS

Modification dependent TagI restriction endonuclease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION7.5294A5 Morpheus Buffer (10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5)
Crystal Properties
Matthews coefficientSolvent content
4.472.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.963α = 90
b = 72.963β = 90
c = 207.576γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294CCDBruker Platinum 135HELIOS multilayer optics2018-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER X8 PROTEUM1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.922096.10.23860.21964.383.2312496
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.923.0296.20.69830.94851.23.3

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 REPLACEMENTTHROUGHOUT3clz, 5mkw2.92201189060796.640.193890.192420.22309RANDOM51.062
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]
1.541.54-3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.393
r_dihedral_angle_4_deg21.054
r_dihedral_angle_3_deg14.906
r_long_range_B_refined7.486
r_long_range_B_other7.481
r_dihedral_angle_1_deg6.271
r_scangle_other4.741
r_mcangle_it4.623
r_mcangle_other4.622
r_mcbond_it2.689
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.393
r_dihedral_angle_4_deg21.054
r_dihedral_angle_3_deg14.906
r_long_range_B_refined7.486
r_long_range_B_other7.481
r_dihedral_angle_1_deg6.271
r_scangle_other4.741
r_mcangle_it4.623
r_mcangle_other4.622
r_mcbond_it2.689
r_mcbond_other2.684
r_scbond_other2.675
r_scbond_it2.674
r_angle_refined_deg1.338
r_angle_other_deg0.932
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms2212
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata reduction
SAINTdata scaling
SADABSdata scaling
PHASERphasing
FFFEARphasing
BALBESphasing
BUCCANEERmodel building
ARP/wARPmodel building