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Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide Dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NOJ PDB ENTRY 1NOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 2.5 M ammonium sulfate, 100mM imidazole/malate buffer, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.626 α = 90 b = 79.626 β = 90 c = 241.612 γ = 120
Symmetry Space Group P 61 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 2 39.57 97.6 0.055 28.6 30942 21.6
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 2 2.13 96.8 0.226 5.4
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 (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 1NOJ 2 39.57 31652 30942 1538 97.6 0.235 0.235 0.2393 0.274 0.2764 RANDOM 33.8
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] -1.5 3.63 -1.5 2.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.21 c_scbond_it 1.63 c_mcangle_it 1.46 c_angle_deg 1.2 c_mcbond_it 0.97 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 2.21 c_scbond_it 1.63 c_mcangle_it 1.46 c_angle_deg 1.2 c_mcbond_it 0.97 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3136 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing CNS refinement HKL-2000 data reduction