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Cambialistic superoxide dismutase from Porphyromonas gingivalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISA PDB ENTRY 1ISA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 SOLUTION CONTAINING 6-9MG/ML PROTEIN AND 10MM TRIS/HCL (PH7.8) WERE USED FOR CRYSTALLIZATION. CRYSTALS WERE GROWN FROM HANGING DROPS SUSPENDED OVER A RESERVOIR SOLUTION CONTAINING 100MM POTASSIUM PHOSPHATE (PH5.8) AND 26-31% PEG4000 AT 293K WITHIN A FEW WEEKS., pH 5.80
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.47 α = 90 b = 102.66 β = 90 c = 99.59 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU IMAGE PLATE YALE MIRRORS 1996-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 1.79 99.4 88.2 0.057 11.6 5.64 64134 22.1
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 1.79 1.86 68.5 0.262 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1ISA 1.8 50 63443 1927 87.7 0.179 0.179 0.1794 0.223 0.2182 RANDOM 31.4
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.9 x_scangle_it 2.337 x_scbond_it 1.573 x_mcangle_it 1.572 x_angle_deg 1.22 x_mcbond_it 0.999 x_improper_angle_d 0.67 x_bond_d 0.006 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.9 x_scangle_it 2.337 x_scbond_it 1.573 x_mcangle_it 1.572 x_angle_deg 1.22 x_mcbond_it 0.999 x_improper_angle_d 0.67 x_bond_d 0.006 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6096 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 4
Software Software Software Name Purpose X-PLOR refinement PROCESS data reduction PROCESS data scaling X-PLOR phasing