☰ Navigation Tabs
Pyrobaculum calidifontis 5-aminolaevulinic 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 7.5 290 Protein buffer was 10 mM Tris-HCl pH 8.0. Protein concentration 5 mg/ml. It was crystallised in the presence of 1 mM levulinic acid with 0.1 M HEPES pH 7.5, 10 % isopropanol and 20 % polyethylene glycol (PEG) 4000 in the well solution.
Crystal Properties Matthews coefficient Solvent content 2.68 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.561 α = 90 b = 205.561 β = 90 c = 199.171 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2013-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.04 Diamond I02
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 3.47 178.02 100 0.118 14.7 9.8 63352 75.9
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 3.47 3.6 100 0.548 4.8 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1b4e 3.47 178.02 60159 3154 99.99 0.1528 0.14762 0.25002 0.2329 RANDOM 92.638
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] -1.02 -0.51 -1.02 3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.622 r_dihedral_angle_3_deg 20.877 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_1_deg 9.463 r_long_range_B_refined 7.735 r_long_range_B_other 7.735 r_mcangle_it 5.045 r_mcangle_other 5.045 r_scangle_other 4.502 r_mcbond_it 2.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.622 r_dihedral_angle_3_deg 20.877 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_1_deg 9.463 r_long_range_B_refined 7.735 r_long_range_B_other 7.735 r_mcangle_it 5.045 r_mcangle_other 5.045 r_scangle_other 4.502 r_mcbond_it 2.966 r_mcbond_other 2.966 r_scbond_it 2.571 r_scbond_other 2.571 r_angle_refined_deg 1.884 r_angle_other_deg 1.161 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 31680 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing MOLREP phasing