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The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6.2 - 6.5, 1.0 - 1.6 M ammonium sulphate and 0 - 10 % dioxane.
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.53 α = 90 b = 125.53 β = 90 c = 200.91 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 180 mm plate 1998-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 0.87 SRS PX9.5
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 2.8 54.2 96 0.071 6 5.9 18652 18652 36.1
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 2.8 3 76.7 0.257 2.9 3.7
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 1aw5 2.83 44.38 17779 872 95.61 0.1687 0.1653 0.1737 0.23785 0.2347 RANDOM 59.13
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] -1.04 -1.04 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_3_deg 18.071 r_dihedral_angle_4_deg 17.986 r_long_range_B_refined 11.049 r_long_range_B_other 11.032 r_scangle_other 7.182 r_mcangle_it 6.674 r_mcangle_other 6.674 r_dihedral_angle_1_deg 6.253 r_scbond_other 4.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_3_deg 18.071 r_dihedral_angle_4_deg 17.986 r_long_range_B_refined 11.049 r_long_range_B_other 11.032 r_scangle_other 7.182 r_mcangle_it 6.674 r_mcangle_other 6.674 r_dihedral_angle_1_deg 6.253 r_scbond_other 4.588 r_scbond_it 4.587 r_mcbond_it 4.163 r_mcbond_other 4.159 r_angle_refined_deg 1.655 r_angle_other_deg 1.224 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 4825 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling