☰ Navigation Tabs
Crystal structure of the double mutant Y88H-P104H of a 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, 30% PEG4000, 0.2M Ammonium Sulphate, 1mM ZnCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.462 α = 90 b = 104.35 β = 90 c = 58.756 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH Double crystal focussing mono chromator 2004-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.27680 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 1.6 28.8 99.6 0.057 0.057 9.1 7 43173 43173 21.907
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 1.6 1.69 99.2 0.478 0.478 1.6 6.9 6245
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 1S4I 1.6 25.6 39853 39853 3320 100 0.25381 0.25381 0.25279 0.2529 0.26628 0.2669 RANDOM 26.866
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] -1.36 2.06 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.982 r_sphericity_free 22.781 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 18.564 r_dihedral_angle_1_deg 17.208 r_scangle_it 3.512 r_scbond_it 2.346 r_angle_refined_deg 1.802 r_mcangle_it 1.662 r_mcbond_it 1.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.982 r_sphericity_free 22.781 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 18.564 r_dihedral_angle_1_deg 17.208 r_scangle_it 3.512 r_scbond_it 2.346 r_angle_refined_deg 1.802 r_mcangle_it 1.662 r_mcbond_it 1.183 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.253 r_xyhbond_nbd_refined 0.235 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.131 r_metal_ion_refined 0.121 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing