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Crystal Structure of SodA-1 (BA4499) from Bacillus anthracis at 1.8A Resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JR9 PDB ENTRY 1JR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 PEG4000, Sodium Acetate trihydrate, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.881 α = 90 b = 60.439 β = 106.3 c = 61.981 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 4 Rh coated Si mirror 2004-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87000 SRS PX9.6
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 1.8 50 98.8 0.084 16.3 3.9 39919 39919
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) 1.8 1.86 89.7 0.748 1.5 3.2 3607
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 PDB ENTRY 1JR9 1.8 31.45 37842 37842 2001 100 0.17203 0.17203 0.16912 0.1805 0.22822 0.2389 RANDOM 24.884
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] 1.29 0.91 -0.98 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.421 r_dihedral_angle_4_deg 16.886 r_dihedral_angle_3_deg 14.716 r_scangle_it 6.747 r_dihedral_angle_1_deg 6.53 r_scbond_it 6.466 r_mcangle_it 2.378 r_mcbond_it 1.657 r_angle_refined_deg 1.449 r_angle_other_deg 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.421 r_dihedral_angle_4_deg 16.886 r_dihedral_angle_3_deg 14.716 r_scangle_it 6.747 r_dihedral_angle_1_deg 6.53 r_scbond_it 6.466 r_mcangle_it 2.378 r_mcbond_it 1.657 r_angle_refined_deg 1.449 r_angle_other_deg 0.98 r_mcbond_other 0.299 r_symmetry_vdw_other 0.237 r_nbd_refined 0.21 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.179 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.155 r_symmetry_vdw_refined 0.135 r_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3195 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing