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Crystal Structure of Adenylosuccinate Lyase (PurB) from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 291 Sodium malonate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.381 α = 90 b = 154.381 β = 90 c = 174.989 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315r Toroidal mirror 2007-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.00040 ESRF ID29
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 50 94.2 0.125 12.1 78074 78074 32.963
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 2.03 42.8 0.753 2.4 1741
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 1C3C 2 43.19 73838 73838 3909 100 0.16504 0.16504 0.16276 0.1864 0.20811 0.2269 RANDOM 32.697
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] 0.46 0.23 0.46 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.868 r_dihedral_angle_3_deg 17.957 r_dihedral_angle_4_deg 16.883 r_sphericity_free 6.644 r_dihedral_angle_1_deg 6.551 r_scangle_it 3.676 r_scbond_it 2.533 r_sphericity_bonded 1.777 r_angle_refined_deg 1.56 r_mcangle_it 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.868 r_dihedral_angle_3_deg 17.957 r_dihedral_angle_4_deg 16.883 r_sphericity_free 6.644 r_dihedral_angle_1_deg 6.551 r_scangle_it 3.676 r_scbond_it 2.533 r_sphericity_bonded 1.777 r_angle_refined_deg 1.56 r_mcangle_it 1.44 r_rigid_bond_restr 1.391 r_mcbond_it 1.217 r_angle_other_deg 1.08 r_symmetry_vdw_refined 0.334 r_mcbond_other 0.293 r_symmetry_vdw_other 0.281 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.227 r_chiral_restr 0.21 r_nbd_other 0.206 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.154 r_nbtor_other 0.092 r_xyhbond_nbd_other 0.074 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7004 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing