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E. coli MaeB PTA domain apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Ammonium sulfate, 0.05 M ADA, 13% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.066 α = 90 b = 130.026 β = 90 c = 169.981 γ = 90
Symmetry Space Group P 21 21 21
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 2022-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 47.88 99.9 0.181 0.196 0.076 0.995 9.8 6.6 59681 138.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.88 100 1.297 1.403 0.531 0.788 1.8 6.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZN9 2.8 47.876 59613 2971 99.915 0.216 0.2142 0.2142 0.2592 0.2541 60.271
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] 0.007 -0.018 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.059 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_4_deg 11.25 r_lrange_it 6.235 r_lrange_other 6.235 r_dihedral_angle_1_deg 4.977 r_mcangle_it 3.434 r_mcangle_other 3.433 r_scangle_it 3.23 r_scangle_other 3.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.059 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_4_deg 11.25 r_lrange_it 6.235 r_lrange_other 6.235 r_dihedral_angle_1_deg 4.977 r_mcangle_it 3.434 r_mcangle_other 3.433 r_scangle_it 3.23 r_scangle_other 3.229 r_angle_other_deg 2.275 r_mcbond_it 2.042 r_mcbond_other 2.042 r_scbond_it 1.85 r_scbond_other 1.849 r_angle_refined_deg 1.218 r_nbd_other 0.4 r_symmetry_nbd_refined 0.309 r_symmetry_nbd_other 0.228 r_nbd_refined 0.199 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.07 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.045 r_bond_other_d 0.034 r_gen_planes_other 0.009 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15407 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing