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Complex of a Mg2-dependent porphobilinogen synthase from Pseudomonas aeruginosa (mutant D139N) with 5-fluorolevulinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR SOLUTION: 1 M NA/K-TARTRATE, 0.2M LI2SO4, 0.1 M CHES PH = 9,5. SITTING DROP: 0.003 ML CRYSTALLISATION SOLUTION + 0.003 ML RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.131 α = 90 b = 127.131 β = 90 c = 86.145 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 MIRRORS 2001-10-15 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 1.66 20 99.9 0.116 11 5.2 82775 3
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 1.66 1.72 100 0.394 4.1 4.9
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B4K 1.66 91.29 78644 4131 99.1 0.175 0.198 RANDOM 20.86
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.142 r_dihedral_angle_1_deg 4.584 r_scangle_it 2.829 r_scbond_it 1.673 r_angle_refined_deg 1.657 r_mcangle_it 1.057 r_angle_other_deg 0.805 r_mcbond_it 0.581 r_xyhbond_nbd_other 0.381 r_symmetry_vdw_refined 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.142 r_dihedral_angle_1_deg 4.584 r_scangle_it 2.829 r_scbond_it 1.673 r_angle_refined_deg 1.657 r_mcangle_it 1.057 r_angle_other_deg 0.805 r_mcbond_it 0.581 r_xyhbond_nbd_other 0.381 r_symmetry_vdw_refined 0.361 r_nbd_refined 0.332 r_metal_ion_refined 0.232 r_symmetry_vdw_other 0.226 r_symmetry_hbond_refined 0.223 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.209 r_chiral_restr 0.151 r_symmetry_hbond_other 0.02 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_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 5050 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing