X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XS1PDB entry 1XS1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52881.9 mg/ml enzyme in 20 mM MgCl2, 5mM dTTP, 50mM HEPES pH 6.8 reservoir solution: 45% PEG 400, 200mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
1.9436.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.64α = 70.75
b = 82.64β = 70.75
c = 82.64γ = 70.75
Symmetry
Space GroupR 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

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
1219.698.10.15915.012223522235-3-322.025
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)
122.197.80.5954.52973

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1XS1219.58222342223411121000.1640.1640.1610.217RANDOM16.975
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]
0.71-1.08-1.080.71-1.080.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.765
r_dihedral_angle_4_deg18.603
r_dihedral_angle_3_deg15.348
r_dihedral_angle_1_deg5.953
r_scangle_it3.299
r_mcangle_it2.995
r_scbond_it2.434
r_mcbond_it2.07
r_angle_refined_deg1.378
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.765
r_dihedral_angle_4_deg18.603
r_dihedral_angle_3_deg15.348
r_dihedral_angle_1_deg5.953
r_scangle_it3.299
r_mcangle_it2.995
r_scbond_it2.434
r_mcbond_it2.07
r_angle_refined_deg1.378
r_nbtor_refined0.32
r_symmetry_vdw_refined0.25
r_symmetry_hbond_refined0.238
r_nbd_refined0.227
r_xyhbond_nbd_refined0.22
r_chiral_restr0.087
r_bond_refined_d0.009
r_metal_ion_refined0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2924
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms84

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction