4GTB

T. Maritima FDTS with FAD, dUMP, and Raltitrexed.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O26PDB ENTRY 1O26

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.582953-6% PEG 4K (w/v), 200mM NaCl, 100 mM Na/K phosphate (pH 6.58), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.3863.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.57α = 90
b = 110.57β = 90
c = 121.73γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirrors2011-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9809SSRLBL9-2

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
11.740990.05216.64125441254
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)
11.71.7499.90.8312.15.33042

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1O261.739.093917439174207599.080.171550.170930.18304RANDOM29.649
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]
-0.67-0.671.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.213
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg14.244
r_dihedral_angle_1_deg6.069
r_scangle_it3.957
r_scbond_it2.566
r_angle_refined_deg1.74
r_mcangle_it1.701
r_angle_other_deg0.963
r_mcbond_it0.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.213
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg14.244
r_dihedral_angle_1_deg6.069
r_scangle_it3.957
r_scbond_it2.566
r_angle_refined_deg1.74
r_mcangle_it1.701
r_angle_other_deg0.963
r_mcbond_it0.909
r_mcbond_other0.278
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1771
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms89

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling