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Crystal Structure of SodA-2 (BA5696) 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, HANGING DROP 8 291 PEG 3350, MgCl2, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.842 α = 90 b = 69.866 β = 106.85 c = 56.574 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 0.071 26.33 3.6 37730 37730
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 94 0.597 1.94 3 3554
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 29.09 35719 35719 1879 100 0.1617 0.1617 0.15872 0.1668 0.21932 0.2254 RANDOM 27.488
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] -0.02 0.09 -0.03 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.477 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_4_deg 12.473 r_sphericity_free 6.776 r_dihedral_angle_1_deg 6.41 r_scangle_it 5.077 r_scbond_it 3.957 r_rigid_bond_restr 3.293 r_sphericity_bonded 2.851 r_mcangle_it 2.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.477 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_4_deg 12.473 r_sphericity_free 6.776 r_dihedral_angle_1_deg 6.41 r_scangle_it 5.077 r_scbond_it 3.957 r_rigid_bond_restr 3.293 r_sphericity_bonded 2.851 r_mcangle_it 2.488 r_mcbond_it 1.883 r_angle_refined_deg 1.444 r_angle_other_deg 0.91 r_mcbond_other 0.697 r_symmetry_hbond_refined 0.249 r_symmetry_vdw_other 0.227 r_nbd_refined 0.213 r_nbtor_refined 0.183 r_nbd_other 0.182 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.097 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3284 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing