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Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D131C)
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 DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (31.5 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 20 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES,HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.22 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.32 α = 90 b = 126.32 β = 90 c = 85.628 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 2002-08-20 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 1.7 20 98.5 0.052 17.8 4.3 75220
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 1.7 1.76 98 0.33 3.2 4.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B4K 1.7 87.71 71529 3768 98.5 0.14 0.138 0.182 RANDOM 18.92
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] 0.15 0.15 -0.31
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.696 r_dihedral_angle_1_deg 6.145 r_scbond_it 5.335 r_mcangle_it 4.335 r_mcbond_it 3.277 r_angle_refined_deg 2.102 r_angle_other_deg 1.017 r_symmetry_vdw_refined 0.479 r_symmetry_vdw_other 0.345 r_nbd_other 0.259
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.696 r_dihedral_angle_1_deg 6.145 r_scbond_it 5.335 r_mcangle_it 4.335 r_mcbond_it 3.277 r_angle_refined_deg 2.102 r_angle_other_deg 1.017 r_symmetry_vdw_refined 0.479 r_symmetry_vdw_other 0.345 r_nbd_other 0.259 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.178 r_chiral_restr 0.164 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.089 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 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 5051 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing