3M9V

X-ray Structure of a KijD3 in Complex with dTDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52981.3-1.6 M Ammonium Sulfate 10 mM dTDP-phenol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4850.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.948α = 90
b = 82.487β = 90
c = 153.22γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277AREA DETECTORSIEMENS HI-STARSupper Mirrors2010-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
12.055094.20.0810.08110.733.492942027721
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)
2.052.1580.70.1960.1963.51.5

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 REPLACEMENTTHROUGHOUTIn-house MIR model2.05502772126300142094.220.171080.16840.22107RANDOM27.914
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]
1.08-0.12-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.216
r_dihedral_angle_4_deg18.061
r_dihedral_angle_3_deg15.898
r_scangle_it6.828
r_dihedral_angle_1_deg6.338
r_scbond_it4.327
r_mcangle_it2.601
r_angle_refined_deg1.995
r_mcbond_it1.697
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.216
r_dihedral_angle_4_deg18.061
r_dihedral_angle_3_deg15.898
r_scangle_it6.828
r_dihedral_angle_1_deg6.338
r_scbond_it4.327
r_mcangle_it2.601
r_angle_refined_deg1.995
r_mcbond_it1.697
r_chiral_restr0.137
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2886
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms25

Software

Software
Software NamePurpose
FRAMBOdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling