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Product-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 293 ALAD at 7 mg per ml mixed with equal volume of well solution: 200 mM Tris pH 8.0 - 8.4, 2 % saturated Ammonium sulphate, 200 microM zinc sulphate, 6 mM beta-mercaptoethanol and 3 mM porphobilinogen. Crystals were grown in the dark.
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.619 α = 90 b = 128.619 β = 90 c = 142.815 γ = 90
Symmetry Space Group I 4 2 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 MAR scanner 345 mm plate 1997-11-06 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 1998-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.069 ESRF BM14 2 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.834 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2 2.07 23.84 95.2 0.078 0.998 15.3 7 34487
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 2.19 68.1 0.368 0.911 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1b4e 2.1 95.57 32987 1761 98.95 0.15953 0.15676 0.1687 0.21285 0.2196 RANDOM 34.462
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] 0.62 0.62 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_3_deg 14.638 r_long_range_B_refined 7.634 r_long_range_B_other 7.391 r_dihedral_angle_1_deg 6.664 r_scangle_other 4.7 r_scbond_it 3.005 r_scbond_other 2.922 r_mcangle_it 2.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_3_deg 14.638 r_long_range_B_refined 7.634 r_long_range_B_other 7.391 r_dihedral_angle_1_deg 6.664 r_scangle_other 4.7 r_scbond_it 3.005 r_scbond_other 2.922 r_mcangle_it 2.894 r_mcangle_other 2.893 r_angle_refined_deg 2.541 r_mcbond_it 1.933 r_mcbond_other 1.933 r_angle_other_deg 1.346 r_chiral_restr 0.162 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2484 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 37
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement