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Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations 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, HANGING DROP 7.5 HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM BETA-MERCAPTOETHANOLE) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 40 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.22 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.322 α = 90 b = 125.322 β = 90 c = 85.795 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 2002-08-21 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 1.65 20 99.4 0.05 20.5 5.4 81768
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 1.65 1.71 99 0.36 3.1 5.1
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 1.65 87.71 76946 4030 98.4 0.152 0.151 0.1647 0.188 0.1975 RANDOM 19.9
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] 0.28 0.28 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.372 r_dihedral_angle_4_deg 18.683 r_dihedral_angle_3_deg 13.599 r_scangle_it 7.787 r_dihedral_angle_1_deg 5.535 r_scbond_it 5.407 r_mcangle_it 4.68 r_mcbond_it 3.521 r_angle_refined_deg 2.105 r_angle_other_deg 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.372 r_dihedral_angle_4_deg 18.683 r_dihedral_angle_3_deg 13.599 r_scangle_it 7.787 r_dihedral_angle_1_deg 5.535 r_scbond_it 5.407 r_mcangle_it 4.68 r_mcbond_it 3.521 r_angle_refined_deg 2.105 r_angle_other_deg 1.146 r_symmetry_vdw_refined 0.302 r_symmetry_vdw_other 0.293 r_nbd_refined 0.239 r_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.165 r_xyhbond_nbd_refined 0.148 r_nbtor_other 0.086 r_bond_refined_d 0.026 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 5001 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing