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Crystal structure of the competence damage-inducible protein A (ComA) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 0.2 M NaCl, 0.1 M Ph-Citrate pH4.2, 20% PEG8K
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.452 α = 90 b = 90.433 β = 103.75 c = 44.126 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 100 PIXEL DECTRIS EIGER X 9M 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07822 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.3 50 97.7 0.062 0.062 0.025 1 29.1 6.3 70520 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.31 99.3 0.876 0.876 0.447 0.653 1.9 4.5
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 2A9S 1.3 45.22 62288 3179 91.17 0.12553 0.12375 0.1356 0.16073 0.1697 RANDOM 18.613
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] 0.45 0.19 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_sphericity_free 28.223 r_dihedral_angle_4_deg 19.422 r_sphericity_bonded 12.366 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 6.073 r_long_range_B_refined 4.792 r_long_range_B_other 4.111 r_scangle_other 4.064 r_scbond_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_sphericity_free 28.223 r_dihedral_angle_4_deg 19.422 r_sphericity_bonded 12.366 r_dihedral_angle_3_deg 11.566 r_dihedral_angle_1_deg 6.073 r_long_range_B_refined 4.792 r_long_range_B_other 4.111 r_scangle_other 4.064 r_scbond_it 3.256 r_scbond_other 3.249 r_mcangle_it 2.28 r_mcangle_other 2.28 r_mcbond_it 1.786 r_mcbond_other 1.786 r_angle_refined_deg 1.45 r_rigid_bond_restr 1.42 r_angle_other_deg 0.932 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing