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Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C, D139C, P132E, K229R)
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 (10 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 MICROM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 80 MM MGCL2, 20MM DTT) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION, IN AN ANAEROBIC BOX.
Crystal Properties Matthews coefficient Solvent content 2.23 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.667 α = 90 b = 125.667 β = 90 c = 85.523 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 2003-11-04 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 1.4 20 99.3 0.06 27.9 9.6 132918
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 1.4 1.45 100 0.56 5.7 9.5
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 1.4 87.71 123617 6524 97.2 0.148 0.147 0.159 0.173 0.1839 RANDOM 16.3
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] 0.31 0.31 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 13.441 r_scangle_it 7.684 r_dihedral_angle_1_deg 6.043 r_scbond_it 5.202 r_mcangle_it 3.982 r_mcbond_it 2.939 r_angle_refined_deg 2.049 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 13.441 r_scangle_it 7.684 r_dihedral_angle_1_deg 6.043 r_scbond_it 5.202 r_mcangle_it 3.982 r_mcbond_it 2.939 r_angle_refined_deg 2.049 r_angle_other_deg 0.926 r_symmetry_vdw_other 0.314 r_symmetry_vdw_refined 0.299 r_nbd_refined 0.236 r_nbd_other 0.211 r_nbtor_refined 0.187 r_chiral_restr 0.145 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.124 r_nbtor_other 0.097 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 4969 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing