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The crystal structure of gene product PA4063 from Pseudomonas aeruginosa
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 293 ammonium sulfate 2M, sodium chloride 2M
Crystal Properties Matthews coefficient Solvent content 2.82 56.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.825 α = 90 b = 65.825 β = 90 c = 101.22 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 PILATUS 6M 2019-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000100 ELETTRA 5.2R
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 1.95 46.55 99.9 0.081 0.088 0.035 0.999 17.3 11.7 16839
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 1.95 2 0.037 0.04 0.015 0.999 8.9
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 1.952 42.324 16788 825 99.857 0.195 0.1934 0.1933 0.2202 0.218 39.707
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] 0.024 0.024 -0.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.393 r_dihedral_angle_4_deg 15.299 r_dihedral_angle_3_deg 15.164 r_lrange_other 10.897 r_lrange_it 10.891 r_scangle_it 9.686 r_scangle_other 9.686 r_scbond_it 6.496 r_scbond_other 6.49 r_dihedral_angle_1_deg 6.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.393 r_dihedral_angle_4_deg 15.299 r_dihedral_angle_3_deg 15.164 r_lrange_other 10.897 r_lrange_it 10.891 r_scangle_it 9.686 r_scangle_other 9.686 r_scbond_it 6.496 r_scbond_other 6.49 r_dihedral_angle_1_deg 6.397 r_mcangle_other 4.676 r_mcangle_it 4.649 r_mcbond_it 3.681 r_mcbond_other 3.636 r_angle_refined_deg 1.835 r_angle_other_deg 1.403 r_symmetry_nbd_refined 0.308 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.157 r_nbd_other 0.126 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1002 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction XDS data scaling MOLREP phasing