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Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C 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 8.5 HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (7.5 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 8.5, 200 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.24 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.307 α = 90 b = 126.307 β = 90 c = 85.156 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 1.6 20 99.9 0.05 32.7 6.4 90595
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 1.6 1.63 100 0.28 5.5 6.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B4K 1.6 87.71 85549 4488 99 0.131 0.129 0.165 0.1769 RANDOM 14.2
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 17.121 r_dihedral_angle_3_deg 13.493 r_scangle_it 6.727 r_dihedral_angle_1_deg 5.767 r_scbond_it 4.679 r_mcangle_it 3.479 r_mcbond_it 2.744 r_angle_refined_deg 2.061 r_angle_other_deg 1.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 17.121 r_dihedral_angle_3_deg 13.493 r_scangle_it 6.727 r_dihedral_angle_1_deg 5.767 r_scbond_it 4.679 r_mcangle_it 3.479 r_mcbond_it 2.744 r_angle_refined_deg 2.061 r_angle_other_deg 1.034 r_symmetry_vdw_other 0.278 r_nbd_refined 0.233 r_nbd_other 0.202 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.176 r_chiral_restr 0.157 r_symmetry_hbond_refined 0.121 r_xyhbond_nbd_refined 0.12 r_nbtor_other 0.086 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 5051 Nucleic Acid Atoms Solvent Atoms 887 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing