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Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C and D139C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4K PDB ENTRY 1B4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M K/NA-TARTRATE, 100MM MES PH 6.0, 20MM BETA-MERCAPTOETHANOLE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC)
Crystal Properties Matthews coefficient Solvent content 2.27 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.991 α = 90 b = 126.991 β = 90 c = 85.369 γ = 90
Symmetry Space Group P 4 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 IMAGE PLATE MARRESEARCH 2002-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 20 99.9 0.1 29.6 14.3 59936
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.31 9.3 14.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B4K 1.85 91.29 56718 3012 99.6 0.134 0.131 0.1464 0.176 0.1868 RANDOM 20.09
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.728 r_dihedral_angle_1_deg 6.022 r_scbond_it 4.646 r_mcangle_it 4.053 r_mcbond_it 3.012 r_angle_refined_deg 2.01 r_angle_other_deg 0.987 r_symmetry_vdw_refined 0.407 r_symmetry_vdw_other 0.342 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.728 r_dihedral_angle_1_deg 6.022 r_scbond_it 4.646 r_mcangle_it 4.053 r_mcbond_it 3.012 r_angle_refined_deg 2.01 r_angle_other_deg 0.987 r_symmetry_vdw_refined 0.407 r_symmetry_vdw_other 0.342 r_nbd_other 0.26 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.153 r_xyhbond_nbd_refined 0.135 r_nbtor_other 0.09 r_bond_refined_d 0.025 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5042 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing