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Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1M Na Acetate, 20% PEG4000, 0.1M Ammonium Sulphate, 10mM ZnCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.147 α = 78.24 b = 56.586 β = 89.91 c = 59.118 γ = 85.47
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 MARRESEARCH Double crystal focussing mono chromator 2004-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.37110 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 38.958 94.2 0.067 0.067 6.9 3 41966 41966 28.733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 92.2 0.244 0.244 2.5 3 5985
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1S4I 2 38.92 38482 38482 3477 100 0.23739 0.23739 0.23186 0.29919 0.276 RANDOM 26.755
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] -0.39 0.02 -0.96 3.01 -0.76 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.144 r_dihedral_angle_3_deg 20.703 r_dihedral_angle_4_deg 19.316 r_sphericity_free 11.2 r_dihedral_angle_1_deg 10.658 r_scangle_it 4.975 r_scbond_it 3.592 r_angle_refined_deg 2.725 r_mcangle_it 2.062 r_mcbond_it 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.144 r_dihedral_angle_3_deg 20.703 r_dihedral_angle_4_deg 19.316 r_sphericity_free 11.2 r_dihedral_angle_1_deg 10.658 r_scangle_it 4.975 r_scbond_it 3.592 r_angle_refined_deg 2.725 r_mcangle_it 2.062 r_mcbond_it 1.407 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.286 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.232 r_chiral_restr 0.213 r_xyhbond_nbd_refined 0.202 r_metal_ion_refined 0.124 r_bond_refined_d 0.03 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4544 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing