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Superoxide dismutase with manganese from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 magnesium chloride, tris-hydrochloride, PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.833 α = 90 b = 83.499 β = 105.79 c = 65.495 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 315 2005-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.5499 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 90 92.6 0.073 20.3297 5.6 11594 11594
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 71.7 0.235 4.7 883
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 1y67 2.7 62.99 11008 11008 572 92.51 0.1701 0.1701 0.16767 0.1804 0.21418 0.2182 RANDOM 61.307
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] -1.11 4.59 -4.47 8.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.663 r_dihedral_angle_3_deg 16.974 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.43 r_scangle_it 2.568 r_angle_refined_deg 1.742 r_scbond_it 1.584 r_mcangle_it 0.991 r_angle_other_deg 0.956 r_mcbond_it 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.663 r_dihedral_angle_3_deg 16.974 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.43 r_scangle_it 2.568 r_angle_refined_deg 1.742 r_scbond_it 1.584 r_mcangle_it 0.991 r_angle_other_deg 0.956 r_mcbond_it 0.805 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.231 r_symmetry_vdw_other 0.208 r_nbtor_refined 0.193 r_nbd_other 0.19 r_symmetry_vdw_refined 0.161 r_mcbond_other 0.145 r_xyhbond_nbd_refined 0.101 r_nbtor_other 0.097 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3287 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection SCALEPACK data scaling EPMR phasing