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5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa
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 (10 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 5 MM 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID SODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (12.0 % (W/V) PEG-8000, 340 MM LI2SO4, 20% (V/V) GLYCEROL,)ABOVE 500 MICROL OF RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.538 α = 90 b = 127.538 β = 90 c = 85.79 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 CCD MARRESEARCH MIRRORS 2005-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.48 38.1 96.2 0.08 19.3 6.8 117544
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 1.48 1.51 98.2 0.36 3.1 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B4K 1.48 90.17 107399 5653 96.2 0.149 0.148 0.1467 0.171 0.1698 RANDOM 11.31
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.107 r_dihedral_angle_4_deg 16.561 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_1_deg 5.4 r_scangle_it 2.232 r_scbond_it 1.486 r_angle_refined_deg 1.249 r_mcangle_it 0.863 r_mcbond_it 0.548 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.107 r_dihedral_angle_4_deg 16.561 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_1_deg 5.4 r_scangle_it 2.232 r_scbond_it 1.486 r_angle_refined_deg 1.249 r_mcangle_it 0.863 r_mcbond_it 0.548 r_nbtor_refined 0.303 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.108 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 5146 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling