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Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation 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 IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.23 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.231 α = 90 b = 125.232 β = 90 c = 86.03 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 RIGAKU R-AXIS IV BLUE OPTIC 2002-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.2 47.1 99.8 0.1 23.1 12.6 35228
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 2.2 2.28 99.5 0.45 5.3 11.8
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 2.2 87.71 33396 1811 99.7 0.157 0.154 0.1644 0.217 0.2172 RANDOM 30.84
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] 0.57 0.57 -1.13
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.203 r_dihedral_angle_1_deg 5.359 r_mcangle_it 4.869 r_scbond_it 4.199 r_mcbond_it 3.553 r_angle_refined_deg 1.928 r_angle_other_deg 1.166 r_symmetry_vdw_other 0.31 r_symmetry_vdw_refined 0.265 r_nbd_other 0.231
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.203 r_dihedral_angle_1_deg 5.359 r_mcangle_it 4.869 r_scbond_it 4.199 r_mcbond_it 3.553 r_angle_refined_deg 1.928 r_angle_other_deg 1.166 r_symmetry_vdw_other 0.31 r_symmetry_vdw_refined 0.265 r_nbd_other 0.231 r_nbd_refined 0.217 r_chiral_restr 0.151 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.128 r_nbtor_other 0.084 r_bond_refined_d 0.026 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 4899 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing