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The crystal structure of gene product PA4063 from Pseudomonas aeruginosa in complex with Zn (space group P65)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ALY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 AS 3M, MPD 1%
Crystal Properties Matthews coefficient Solvent content 3.77 67.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.005 α = 90 b = 122.005 β = 90 c = 102.263 γ = 120
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 PILATUS3 6M 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.27110 ELETTRA 11.2C
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 3.3 46.94 96.1 0.135 0.143 0.047 0.999 18.6 17.7 12599
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 3.3 3.57 2.461 2.608 0.86 0.677 17.9
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 7ALY 3.301 46.94 12561 552 96.039 0.179 0.1773 0.1752 0.2114 0.2066 133.913
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] 2.683 1.342 2.683 -8.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.671 r_lrange_other 23.304 r_lrange_it 23.295 r_scangle_it 20.521 r_scangle_other 20.521 r_dihedral_angle_3_deg 19.897 r_mcangle_it 18.69 r_mcangle_other 18.687 r_dihedral_angle_4_deg 17.324 r_scbond_it 14.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.671 r_lrange_other 23.304 r_lrange_it 23.295 r_scangle_it 20.521 r_scangle_other 20.521 r_dihedral_angle_3_deg 19.897 r_mcangle_it 18.69 r_mcangle_other 18.687 r_dihedral_angle_4_deg 17.324 r_scbond_it 14.476 r_scbond_other 14.444 r_mcbond_it 13.817 r_mcbond_other 13.794 r_dihedral_angle_1_deg 7.803 r_angle_refined_deg 1.785 r_angle_other_deg 1.182 r_symmetry_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.214 r_nbd_other 0.211 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.16 r_ncsr_local_group_2 0.118 r_xyhbond_nbd_refined 0.113 r_ncsr_local_group_1 0.113 r_ncsr_local_group_3 0.11 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3192 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data processing XDS data reduction XSCALE data scaling AutoSol phasing