X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8FYeiK PDB code 1Q8F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298MPD, Sodium Acetate, ribose, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.651.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.466α = 90
b = 84.062β = 90
c = 112.483γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.782597.80.11626.212.53405634056-3-318
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8677.40.4752.92669

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 REPLACEMENTTHROUGHOUTYeiK PDB code 1Q8F1.78253405634056108697.80.16810.168110.167330.19276RANDOM17.623
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]
0.62-0.790.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.275
r_scangle_it4.618
r_scbond_it2.862
r_mcangle_it1.743
r_angle_refined_deg1.305
r_mcbond_it1
r_nbd_refined0.191
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.275
r_scangle_it4.618
r_scbond_it2.862
r_mcangle_it1.743
r_angle_refined_deg1.305
r_mcbond_it1
r_nbd_refined0.191
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.093
r_chiral_restr0.072
r_metal_ion_refined0.06
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing