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Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen
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 7 289 90% PACT SCREEN CONDITION E4 + 10% ADDIT SCREEN D7: 0.18 M KSCN, 18% PEG 3350, 3% W/V DIAMINOOCTANE, 5 MM AMINOLEVULINIC ACID, TOGOA.17087.A.Y2 AT 6.3 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 7.00, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.11 α = 90 b = 187.17 β = 90 c = 95.86 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315 2010-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
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 2.5 49.93 98.6 0.115 11.8 4.04 110745 109171 -3 31.45
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 2.5 2.56 90.3 0.538 2.3 3.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1B4K 2.5 49.93 110745 108861 5439 0.18 0.18 0.177 0.1792 0.232 0.2281 RANDOM 23.16
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] 1.7 -1.25 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_dihedral_angle_4_deg 20.266 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.107 r_scangle_it 2.816 r_scbond_it 1.678 r_angle_refined_deg 1.497 r_mcangle_it 0.974 r_angle_other_deg 0.928 r_mcbond_it 0.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_dihedral_angle_4_deg 20.266 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.107 r_scangle_it 2.816 r_scbond_it 1.678 r_angle_refined_deg 1.497 r_mcangle_it 0.974 r_angle_other_deg 0.928 r_mcbond_it 0.503 r_mcbond_other 0.123 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21476 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 228
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling