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5-hydroxy-levulinic 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 HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 MICROL RESERVOIR SOLUTION 9.0 % (W/V) PEG-4000, 0.180 M KCL, 0.009 M CACL2, 0.05 M NA-CACODYLATE PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.314 α = 90 b = 126.314 β = 90 c = 85.481 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-MSC R-AXIS IV BLUE OPTIC 2005-01-31 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 2.15 40.2 99.5 0.13 16.7 11 37881 22.5
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 2.15 2.23 99.2 0.46 4.9 9.9
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-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 2.15 89.8 37848 1931 99.2 0.155 0.152 0.1533 0.204 0.2046 RANDOM 17.69
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] -0.047 -0.047 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 20.346 r_dihedral_angle_3_deg 15.736 r_dihedral_angle_1_deg 9.615 r_scangle_it 3.586 r_scbond_it 2.407 r_angle_refined_deg 1.696 r_mcangle_it 1.262 r_mcbond_it 0.725 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 20.346 r_dihedral_angle_3_deg 15.736 r_dihedral_angle_1_deg 9.615 r_scangle_it 3.586 r_scbond_it 2.407 r_angle_refined_deg 1.696 r_mcangle_it 1.262 r_mcbond_it 0.725 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.226 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.13 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 5161 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling