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Crystal Structure of PduA with edge mutation K26A and pore mutation S40C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGK PDB ENTRY 3NGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.5M Ammonium sulfate, 0.1M HEPES pH 7.5, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.68 66.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 235.44 α = 90 b = 235.44 β = 90 c = 235.44 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2014-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9789 APS 24-ID-C
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 3.297 83.24 99.7 0.163 32.47 16403 16403 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.297 3.38 99.8 4.24 1218
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3NGK 3.297 83.24 16365 16365 1637 99.68 0.1932 0.1889 0.1926 0.2317 0.2283 RANDOM 94.737
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_3_deg 19.653 r_dihedral_angle_4_deg 17.779 r_mcangle_it 12.466 r_mcbond_it 8.342 r_mcbond_other 8.338 r_dihedral_angle_1_deg 6.886 r_angle_refined_deg 1.889 r_angle_other_deg 1.801 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_3_deg 19.653 r_dihedral_angle_4_deg 17.779 r_mcangle_it 12.466 r_mcbond_it 8.342 r_mcbond_other 8.338 r_dihedral_angle_1_deg 6.886 r_angle_refined_deg 1.889 r_angle_other_deg 1.801 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4283 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XSCALE data scaling