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Crystal structure of UipA in complex with Uranium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ATH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 MES pH6 100mM, PEG6K 22%, Formamide 6%, ZnCl2 5-15mM
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.16 α = 90 b = 95.16 β = 90 c = 52.51 γ = 90
Symmetry Space Group P 43 21 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 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.3051 SOLEIL PROXIMA 1
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 2.85 47 99.6 0.99 12.2 14 10684
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 2.85 3.03 0.76
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7ATH 2.855 47 5956 298 99.649 0.208 0.207 0.234 0.2244 80.529
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] -2.794 -2.794 5.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 50.078 r_dihedral_angle_4_deg 20.546 r_dihedral_angle_3_deg 20.47 r_lrange_it 16.555 r_lrange_other 16.547 r_scangle_it 14.273 r_scangle_other 14.262 r_mcangle_other 10.598 r_mcangle_it 10.585 r_scbond_it 9.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 50.078 r_dihedral_angle_4_deg 20.546 r_dihedral_angle_3_deg 20.47 r_lrange_it 16.555 r_lrange_other 16.547 r_scangle_it 14.273 r_scangle_other 14.262 r_mcangle_other 10.598 r_mcangle_it 10.585 r_scbond_it 9.552 r_scbond_other 9.546 r_dihedral_angle_1_deg 9.082 r_mcbond_it 7.121 r_mcbond_other 7.069 r_angle_refined_deg 1.782 r_angle_other_deg 1.286 r_symmetry_xyhbond_nbd_refined 0.334 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.185 r_nbd_other 0.179 r_nbtor_refined 0.152 r_metal_ion_refined 0.142 r_xyhbond_nbd_other 0.125 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 962 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing