3ZDE | pdb_00003zde

Potassium free structure of E. coli ExoIX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherEXOIX P21 STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M SODIUM ACETATE TRIHYDRATE, 20% PEG 3350, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.451α = 90
b = 37.432β = 117.41
c = 66.698γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.454092.40.127.91.996926
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)
12.452.58950.413.41.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEXOIX P21 STRUCTURE2.4520855847485.20.177280.172250.180.2730.27RANDOM40.536
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]
-0.42-0.110.85-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.556
r_scbond_it23.53
r_scangle_it22.647
r_mcbond_other22.249
r_mcangle_it20.202
r_mcbond_it19.838
r_dihedral_angle_3_deg15.44
r_dihedral_angle_4_deg11.052
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.556
r_scbond_it23.53
r_scangle_it22.647
r_mcbond_other22.249
r_mcangle_it20.202
r_mcbond_it19.838
r_dihedral_angle_3_deg15.44
r_dihedral_angle_4_deg11.052
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.081
r_angle_other_deg0.858
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1895
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing