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Potassium bound structure of E. coli ExoIX in P21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZD8 PDB ENTRY 3ZD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M SODIUM THIOCYANATE, 10MM ZNCL2 20% PEG 3350, 0.1 M MES AT PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.11 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.472 α = 90 b = 38.275 β = 107.95 c = 59.75 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 40 89 0.09 11.4 2.9 14512 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 85.3 0.37 4.5 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ZD8 2 19.87 13356 714 89 0.16337 0.15881 0.1651 0.24589 0.2452 RANDOM 25.98
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 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 80.766 r_mcbond_it 42.965 r_dihedral_angle_2_deg 39.292 r_mcangle_it 39.218 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.345 r_mcbond_other 1.834 r_angle_refined_deg 1.421 r_angle_other_deg 0.944
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 80.766 r_mcbond_it 42.965 r_dihedral_angle_2_deg 39.292 r_mcangle_it 39.218 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 5.345 r_mcbond_other 1.834 r_angle_refined_deg 1.421 r_angle_other_deg 0.944 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1946 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing