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Crystal structure of Klebsiella pneumoniae ZapA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.2 M Sodium acetate trihydrate, 0.1 M Sodium citrate pH5.5, and 10% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.173 α = 90 b = 54.173 β = 90 c = 330.044 γ = 120
Symmetry Space Group P 61 2 2
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 16M 2023-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 46.45 99.84 0.999 20.03 9 28055
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 0.872
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 46.448 28052 1361 99.868 0.22 0.2186 0.2277 0.2393 0.2515 41.009
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] 0.008 0.004 0.008 -0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.849 r_dihedral_angle_6_deg 15.807 r_dihedral_angle_2_deg 10.576 r_lrange_it 9.919 r_lrange_other 9.875 r_scangle_it 8.641 r_scangle_other 8.638 r_scbond_it 5.891 r_scbond_other 5.847 r_mcangle_other 5.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.849 r_dihedral_angle_6_deg 15.807 r_dihedral_angle_2_deg 10.576 r_lrange_it 9.919 r_lrange_other 9.875 r_scangle_it 8.641 r_scangle_other 8.638 r_scbond_it 5.891 r_scbond_other 5.847 r_mcangle_other 5.083 r_mcangle_it 5.077 r_dihedral_angle_1_deg 4.387 r_mcbond_it 3.911 r_mcbond_other 3.904 r_angle_refined_deg 1.53 r_angle_other_deg 0.807 r_symmetry_nbd_refined 0.337 r_nbd_other 0.264 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.177 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1712 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing