3ZD9 | pdb_00003zd9

Potassium bound structure of E. coli ExoIX in P21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZD8PDB ENTRY 3ZD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M SODIUM THIOCYANATE, 10MM ZNCL2 20% PEG 3350, 0.1 M MES AT PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.472α = 90
b = 38.275β = 107.95
c = 59.75γ = 90
Symmetry
Space GroupP 1 21 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
1240890.0911.42.9145122
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)
122.0585.30.374.52.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZD8219.8713356714890.163370.158810.170.245890.25RANDOM25.98
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]
0.06-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it80.766
r_mcbond_it42.965
r_dihedral_angle_2_deg39.292
r_mcangle_it39.218
r_dihedral_angle_4_deg15.826
r_dihedral_angle_3_deg14.307
r_dihedral_angle_1_deg5.345
r_mcbond_other1.834
r_angle_refined_deg1.421
r_angle_other_deg0.944
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it80.766
r_mcbond_it42.965
r_dihedral_angle_2_deg39.292
r_mcangle_it39.218
r_dihedral_angle_4_deg15.826
r_dihedral_angle_3_deg14.307
r_dihedral_angle_1_deg5.345
r_mcbond_other1.834
r_angle_refined_deg1.421
r_angle_other_deg0.944
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.006
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_it
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 Atoms1946
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing