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The crystal structure of gene product PA4063 from Pseudomonas aeruginosa in complex with zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 ammonium sulfate 2.3M, NaCl 2.1M
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.467 α = 90 b = 62.467 β = 90 c = 102.076 γ = 90
Symmetry Space Group P 41 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 EIGER2 X 4M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96770 ESRF ID30B
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 2.85 62.47 99.6 0.203 0.212 0.062 0.989 12.5 20.5 5107
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 2.85 3 3.102 3.249 0.962 0.518 20.7
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 7AHW 2.85 44.21 5071 258 99.49 0.188 0.1849 0.1892 0.2369 0.2285 81.095
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] -1.738 -1.738 3.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.522 r_dihedral_angle_3_deg 21.104 r_dihedral_angle_4_deg 19.687 r_lrange_other 15.739 r_lrange_it 15.727 r_scangle_it 13.411 r_scangle_other 13.405 r_mcangle_other 8.876 r_mcangle_it 8.856 r_scbond_it 8.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.522 r_dihedral_angle_3_deg 21.104 r_dihedral_angle_4_deg 19.687 r_lrange_other 15.739 r_lrange_it 15.727 r_scangle_it 13.411 r_scangle_other 13.405 r_mcangle_other 8.876 r_mcangle_it 8.856 r_scbond_it 8.802 r_scbond_other 8.799 r_dihedral_angle_1_deg 8.498 r_mcbond_it 6.246 r_mcbond_other 6.194 r_angle_refined_deg 1.686 r_angle_other_deg 1.164 r_nbd_refined 0.202 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.153 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.12 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.059 r_bond_refined_d 0.017 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 1058 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data processing XDS data reduction XSCALE data scaling MOLREP phasing