5JTG

Crystal structure of Thermotoga maritima mutant D89K/D253K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IUB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62940.2 M Mg(HCO2)2, 0.1 M MES, pH 6.0, 25% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.4264

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.125α = 90
b = 104.488β = 106.13
c = 122.821γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.0547.899.20.0830.99911.33.856456
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)
13.053.2398.11.54413.8

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 REPLACEMENTTHROUGHOUT2IUB3.0547.7753629282399.290.247740.245520.29062RANDOM126.119
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]
-3.68-6.181.223.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.535
r_dihedral_angle_4_deg17.582
r_dihedral_angle_3_deg15.859
r_long_range_B_refined15.087
r_long_range_B_other15.087
r_dihedral_angle_1_deg9.793
r_scangle_other9.146
r_mcangle_it8.412
r_mcangle_other8.411
r_scbond_it5.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.535
r_dihedral_angle_4_deg17.582
r_dihedral_angle_3_deg15.859
r_long_range_B_refined15.087
r_long_range_B_other15.087
r_dihedral_angle_1_deg9.793
r_scangle_other9.146
r_mcangle_it8.412
r_mcangle_other8.411
r_scbond_it5.572
r_scbond_other5.572
r_mcbond_other5.252
r_mcbond_it5.251
r_angle_refined_deg1.099
r_angle_other_deg0.831
r_chiral_restr0.056
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.003
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 Atoms13335
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction