3QSB

Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MMIPDB ENTRY 1MMI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5294100mM Na MES pH 6.0, 50-60mM CaCl2, 30%(v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4249.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.176α = 90
b = 66.519β = 115.86
c = 83.117γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrors2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.92594.80.24313.85796957969-4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9787.92.735356

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 1MMI1.924.695495754957290293.650.246210.246210.242490.31701RANDOM24.483
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]
-0.67-0.131.55-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.206
r_dihedral_angle_4_deg20.834
r_dihedral_angle_3_deg20.726
r_dihedral_angle_1_deg9.034
r_scangle_it5.44
r_scbond_it3.424
r_angle_refined_deg2.205
r_mcangle_it2.172
r_mcbond_it1.233
r_chiral_restr0.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.206
r_dihedral_angle_4_deg20.834
r_dihedral_angle_3_deg20.726
r_dihedral_angle_1_deg9.034
r_scangle_it5.44
r_scbond_it3.424
r_angle_refined_deg2.205
r_mcangle_it2.172
r_mcbond_it1.233
r_chiral_restr0.175
r_bond_refined_d0.023
r_gen_planes_refined0.01
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 Atoms5686
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms64

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling